Method for prophylaxis and/or treatment of ErbB2 positive cancers

ABSTRACT

Provided are compositions and methods for prophylaxis and/or therapy of ErbB2-positive cancer. The compositions include pharmaceutical preparations that contain isolated or recombinant or modified peptidase D (PEPD) proteins. The methods include prophylaxis and/or therapy of ErbB2-positive cancer by administering a PEPD to an individual who has or is at risk for developing ErbB2-positive cancer.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. application No. 61/870,054,filed on Aug. 26, 2013, the disclosure of which is incorporated hereinby reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under contract nos.R01CA120533, R01CA24627 and R01CA164574 awarded by the National CancerInstitute. The government has certain rights in the invention.

FIELD OF THE DISCLOSURE

The present invention relates generally to the field of human health,and in particular to methods for the prophylaxis and treatment ofcancers and/or other conditions that are positively correlated with theexpression of ErbB2.

BACKGROUND OF THE INVENTION

ErbB2, also known as v-erb-b2 avian erythroblastic leukemia viraloncogene homolog 2, Her2, Neu, CD340, proto-oncogene C-ErbB2, is amember of the extensively studied ErbB family of plasma membrane-boundreceptor tyrosine kinases, which also includes ErbB1, ErbB3 and ErbB4(also known as EGFR/Her1, Her3 and Her4, respectively). These receptorshave been shown to play critical roles in embryonic development, normalphysiology and the development of various diseases. All four ErbBreceptors contain an extracellular domain (ECD), a transmembrane domainand an intracellular domain that interacts with signaling molecules.Ligand binding to the ECDs of these receptors leads to homo- orhetero-dimerization, followed by the activation of the intrinsic proteintyrosine kinase and tyrosine autophosphorylation in the intracellulardomain, and recruitment and activation of signaling proteins to thesesites. Notably, ErbB3 is kinase-impaired and requires heterodimerizationfor activation. To date, while multiple ligands have been identified forErbB1, ErbB3 and ErbB4, no ligand for ErbB2 has been found, ever sinceits discovery nearly 30 years ago (Coussens et al. Science 1985; 230:1132-1139; Schechter et al. Science 1985; 229: 976-978). However, ErbB2is a preferred dimerization partner for other ligand-bound ErbBs.

ErbB2 is best known for its involvement in human breast cancer. ErbB2gene amplification occurs in 20-30% of breast cancer and issignificantly correlated with ErbB2 protein expression in the cancertissues. ErbB2 gene amplification or protein overexpression is a strongpredictor of poor disease prognosis. ErbB2-targeted therapies,particularly humanized monoclonal antibody trastuzumab in combinationwith chemotherapy, show considerable clinical efficacy. However, manyErbB2-positive cancers show de novo resistance or acquired resistance tosuch a therapy. Thus, there is an ongoing and unmet need to identify aligand of ErbB2 and to develop therapeutic approaches based at least inpart upon such a ligand. The present disclosure meets these needs.

SUMMARY OF THE DISCLOSURE

The present disclosure provides compositions and methods useful forprophylaxis and/or therapy of ErbB2-positive cancers. The compositionsand methods relate to the present discovery that prolidase is a ligandof the ErbB2 receptor. Further, this disclosure is believed to be thefirst description of any ErbB2 ligand.

Prolidase, also known as peptidase D (PEPD), Xaa-Pro dipeptidase orproline dipeptidase, or imidodipeptidase, is a protease which hydrolyzesdipeptides with proline or hydroxyproline at the carboxy terminus. PEPDis a ubiquitously expressed cytosolic protein and exists as a homodimer(monomeric molecular weight of human PEPD: 54 kD; 493 amino acids asshown in SEQ ID NO:1, which provides the amino acid sequence of humanprolidase.). In embodiments, the PEPD that is used for the compositionsand methods of the instant disclosure is a mammalian PEPD. In oneembodiment, the PEPD is human PEPD. In embodiments, the PEPD can beenzymatically active or have reduced or have no detectable enzymaticactivity.

The compositions comprise pharmaceutical preparations which contain anisolated and/or purified PEPD or recombinant and/or modified PEPD, andcan further comprise additional agents, such as a coagulation inhibitor.In embodiments the PEPD is modified. In embodiments, the PEPD is acomponent of a fusion protein. In embodiments, the fusion proteincomprises the PEPD and an amino acid sequence useful for purification ofrecombinantly produced PEPD.

The methods comprise administering to an individual in need ofprophylaxis and/or therapy of an ErbB2-positive cancer a compositioncomprising a PEPD of this disclosure, and can further compriseadministering to the individual a coagulation inhibitor. Also providedare methods for identifying individuals in need of treatment with PEPDformulations, and methods for generating a treatment protocol for suchindividuals.

In embodiments the disclosure further provides products comprisingpharmaceutical preparations which contain an isolated and/or purifiedPEPD or recombinant PEPD, and which can also contain printed materialdescribing use of the preparations for prophylaxis and/or therapy ofErbB2-positive cancers. In embodiments, the products also contain acoagulation inhibitor. In non-limiting embodiments, the ErbB2-positivecancers are breast, ovarian, stomach, or aggressive forms of uterinecancer, such as uterine serous endometrial carcinoma. In embodiments,ErbB2-positive cancer cells are cancer cells which overexpress ErbB2 orcarry a higher copy number of the ERBB2 gene relative to a non-cancercell. In embodiments, ErbB2-positive cancer cells are cells whichexpress more ErbB2 than a reference, such as a cell of the same typethat is not cancerous.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Data demonstrating that PEPD binds to subdomain 3 of ErbB2 ECDand rapidly promotes ErbB2 dimerization. (a) PEPD at 0.04 μM (+), 0.2 μM(++) or 1 μM (+++) was incubated with ErbB2/ECD-Fc (0.04 μM),ErbB3/ECD-Fc (0.04 μM), ErbB4/ECD-Fc (0.04 μM) or Fc (0.04 μM), pulleddown with protein G-sepharose, separated by SDS-PAGE, and stained withsilver. (b) CHO-K1 cells were transfected with pCMV6-XL5-ERBB2 or theempty vector; 24 h later, cell lysates were prepared and analyzed bywestern blotting. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) wasused here and elsewhere as a loading control. (c) PEPD binding to ErbB2,measured by ELISA (n=3), using cell lysates from b; same amount oflysates for all samples (25 μg protein per sample). Error bars indicateSD. (d) ErbB2 and its mutants; all gene transfections used the sameamount of DNA and lasted for 24 h. Cell lysates were analyzed by westernblotting. (e) PEPD binding to ErbB2 and its mutants, measured by ELISA(n=3), using cell lysates from d and an equal amount of ErbB2 or itsmutants. Error bars indicate SD. (f) CHO-K1 cells stably overexpressingErbB2 (CHO-K1/ErbB2 cells) were treated with PEPD. PEPD-treated cellsand control cells were then treated with cross-linkerbis(sulfosuccinimidyl)suberate (BS3) (2 mM, 30 min). Cell lysates wereanalyzed by western blotting using an ErbB2 antibody.

FIG. 2. Data showing ErbB2 Activation and depletion by PEPD. (a-c) Cellswere treated with PEPD or vehicle; cell lysates were analyzed by westernblotting. (d) Cells were treated with or without PEPD (270 nM), using4-aminophenylmercuric acid (APMA) (1 mM) as a positive control. Celllysates and media were analyzed by western blotting. (e) Cells weretreated with or without PEPD (2.7 nM, 6 h), from which total RNA wasisolated for RT-PCR. GAPDH was used as a control. (f) Cells were treatedwith or without PEPD (270 nM), followed by immunofluorescence stainingof ErbB2 and PEPD and confocal microscopy. Scale bar: 10 μm. (g) Cellswere transfected with ubiquitin (pMT107-His-Ub) and 24 h later treatedwith or without PEPD (2.7 nM, 0.5 h). Cell lysates were incubated withan ErbB2 antibody, pulled down with protein G-agarose, and analyzed bywestern blotting.

FIG. 3. Data showing PEPD directly activates ErbB2, but its dipeptidasefunction is not involved. (a) CHO-K1 cells were transfected with ErbB2or a mutant (all carried by pCMV6-XL5) and 24 h later treated withvehicle or PEPD. Cell lysates were analyzed by western blotting. (b)CHO-K1 cells were transfected with ErbB2 and 24 h later treated withvehicle, PEPD or its mutants. Further information on the mutants isprovided in FIG. 10. Cell lysates were analyzed by western blotting.

FIG. 4. Data showing lack of effect of intracellular PEPD on ErbB2, butPEPD is released from cell. (a) Cells were transfected with a plasmidexpressing human PEPD (pCMV6-XL5-PEPD) or the empty vector for 24 h.Cell lysates were analyzed by western blotting. (b) Cells weretransfected with human PEPD or the empty vector; 24 h later, the cellswere washed and cultured in fresh medium (˜1×10⁶ cell/2 ml medium) foranother 24 h, followed by collection of both cells and the medium. PEPDlevels in the cell lysates were measured by western blotting, and PEPDconcentration in the medium was measured by ELISA (n=3). Error barsindicate SD.

FIG. 5. Data showing that PEPD silences ErbB2-Src signaling. (a, b)Cells were treated with solvent or PEPD (2.7 nM). Cell lysates wereanalyzed by western blotting. (c) Cells were treated with or withoutPEPD (2.7 nM, 0.5 h). Cell lysates were incubated with an ErbB2antibody, pulled down with protein G-agarose, and analyzed by westernblotting. (d) Cells were treated with or without PEPD (2.7 nM) and thenmeasured for Src kinase activity and PI3K activity in the cell lysates(n=3). Error bars indicate SD. (e) Cells were treated with or withoutPEPD (2.7 nM). Cell lysates were analyzed by western blotting. (f) Cellswere treated with pervanadate (30 μM, 10 min) and then treated with orwithout PEPD (2.7 nM, 0.5 h). Cell lysates were incubated with a PTENantibody, pulled down with protein G-agarose, and analyzed by westernblotting. (g) Cells were treated with solvent or PEPD (2.7 nM, 1 h);cytosolic fraction and membrane fraction were prepared and analyzed bywestern blotting. Both GAPDH and pro-TGFα were used as loading controls.

FIG. 6. Graphic showing paradigm of ErbB2 modulation by PEPD, and datashowing selective inhibition of cells overexpressing ErbB2 by PEPD. (a)Both monomers and tyrosine-phosphorylated dimers exist in cellsoverexpressing ErbB2. PEPD binds to ErbB2 as a homodimer; each PEPDsubunit binds to one ErbB2 ECD subdomain 3. PEPD rapidly binds to ErbB2dimers, silencing ErbB2-Src signaling by causing Src disassociation fromErbB2. PEPD binds to ErbB2 monomers somewhat slowly but causes ErbB2dimerization and phosphorylation, leading to activation of downstreamsignaling. PEPD also causes strong and persistent ErbB2 depletionresulting from PEPD-induced ErbB2 internalization and degradation. (b)Cells growing in 6-well plates were treated with vehicle or PEPD for 48h and then measured for DNA synthesis by BrdU incorporation. (c) Cellsgrowing in soft agar in 6-well plates were treated with vehicle or PEPDfor 21 days (with medium change every 3-4 days) and then examined forcolony formation. (d) Cells growing in invasion chambers were treatedwith vehicle or PEPD for 48 hours; cells that invaded through a Matrigelmembrane were counted. Error bars in b-d indicate SD (n=3).

FIG. 7. Data showing binding of neuregulin-1 (NRG-1) to the ECDs ofErbB3 and ErbB4. NRG-1 at 0.2 μM was incubated with Fc (0.04 μM),ErbB3/ECD-Fc (0.04 μM) or ErbB4/ECD-Fc (0.04 μM), pulled down withprotein G-sepharose, separated by SDS-PAGE (15%), and stained withsilver. This demonstrates that both ErbB3/ECD-Fc and ErbB4/ECD-Fc werebiologically functional with regarding to the results shown in FIG. 1.

FIG. 8. Data showing validation of a cell line used in the presentdisclosure, and lack of binding of PEPD to the transmembrane andintracellular regions of human ErbB2. (a) CHO-K1 cells were transientlytransfected with an ErbB2-expressing plasmid (pCMV6-XL5-ERBB2) or theempty plasmid for 24 h. Human bladder cancer RT-4 cells and human breastcancer MCF-7 cells were untreated and were used as positive controls forErbB1, ErbB3 and ErbB4. Cell lysates were analyzed by western blotting.GAPDH is a loading control. (b) CHO-K1 cells stably expressing ErbB2(CHO-K1/ErbB2 cells) were treated with 1 mM APMA for 0.25 h. Celllysates were then prepared and analyzed by western blotting (the firstlane on the right). The same cell lysates were mixed with 1 μM PEPD,which were then incubated with a PEPD antibody or an isotype-matchedIgG, pulled down with protein G-agarose, and analyzed by westernblotting. The result shows that APMA causes ErbB2 ECD cleavage, asexpected, generating the p95 fragment (minus ECD), but PEPD onlyco-precipitates with the intact ErbB2, not the p95 fragment, indicatingthat PEPD does not bind to the trans-membrane or intracellular regionsof ErbB2.

FIG. 9. No effects of epidermal growth factor (EGF) and NRG-1 on ErbB2.(a, b) CHO-K1 cells stably overexpressing human ErbB2 (CHO-K1/ErbB2cells) were treated with recombinant EGF or recombinant NRG-1. Cellslysates were then prepared and analyzed by western blotting. (c, d) Inorder to ensure that both EGF (ligand of ErbB1) and NRG-1 (ligand ofErbB3 and ErbB4) that were used in our experiments were bioactive, theywere evaluated in BT-474 cells, which expressed relatively low levels ofErbB1 and ErbB3. As expected, EGF significantly stimulated ErbB1phosphorylation, and NRG-1 significantly stimulated ErbB3phosphorylation.

FIG. 10. Data showing configuration of human PEPD and its mutants. (a)Wild-type human PEPD and amino acid (aa) changes in its mutants. (b)Recombinant wild-type human PEPD and its mutants were generated inbacteria, purified using nickel affinity chromatography and analyzed bynon-reducing SDS-PAGE and silver staining. Note: Protein loading variedacross the lanes. In the lane indicated by “WT-PEPD+βME”, the wild-typePEPD was incubated with 10% β-mercaptoethanol in PBS before non-reducinggel electrophoresis.

FIG. 11. Data showing ErbB2 distribution in cells. Membrane fraction andlysates minus membrane were prepared from CHO-K1 cells that eitherstably overexpressed human ErbB2 (CHO-K1/ErbB2 cells) or weretransiently transfected with ErbB2 (pCMV6-XL5-ERBB2) for 24 h, and wereanalyzed by western blotting. GAPDH and pro-TGF-α were used as loadingcontrols. Notably, in the experiments described above (see FIG. 3), PEPDor its G278D mutant did not cause decrease in ErbB2 protein level,whereas PEPD caused pronounced ErbB2 depletion in cells stably orconstitutively overexpressing ErbB2 (see FIGS. 2a and 2c ). We foundthat in CHO-K1 cells transiently overexpressing ErbB2, the majority ofErbB2 molecules resided intracellularly, whereas in CHO-K1 cells stablyoverexpressing ErbB2, the majority of ErbB2 molecules were expressed oncell surface, as shown here. This explains why PEPD treatment for 3 hdid not cause clear ErbB2 protein decrease in cells transientlyoverexpressing ErbB2 (see FIG. 3).

FIG. 12. Data showing that induction of ERK phosphorylation by PEPD inCHO-K1 cells depends on ErbB2. CHO-K1 cells were transiently transfectedwith wild-type human ErbB2 or a kinase-dead mutant (ErbB2/K753M) for 24h and then treated with PEPD or vehicle, followed by western blotting.

FIG. 13. Data showing the growth-inhibitory effects of PEPD, G278D-PEPDand trastuzumab on cells with or without ErbB2 overexpression. Cellswere grown in 96-well plates (500 CHO-K1 cells or CHO-K1/ErbB2 cells perwell or 2,000 BT-474 cells per well; 150 μl medium per well) overnightand then treated with vehicle, PEPD, G278D-PEPD or trastuzumab in 200 μlmedium per well for 72 h, followed by incubation withmethylthiazolyldiphenyl-tetrazolium bromide (MTT) (9.2 mM in medium) at37° C. for 3 h. After removing the medium, the cells were treated withdimethyl sulfoxide (150 μl per well), and the cell density wasdetermined by measuring formazan formed from MTT spectroscopically at570 nm (n=3). The error bars indicate SD.

FIG. 14. Data showing the impact of a blood coagulation inhibitor onplasma levels of PEPD. (a) Recombinant human PEPD was administered tomice by intraperitoneal injection at 0.2 mg/kg body weight or 10 mg/kg;mice were killed at 1, 6 or 24 h after PEPD dosing, and plasma level ofPEPD was measured by ELISA along with that in the control mice. (b)Enoxaparin (EP), a blood coagulation inhibitor, was administered to miceby intraperitoneal injection at 2.5 mg/kg once daily; 1 h after thefourth EP dose, PEPD was administered to the mice by intraperitonealinjection at 0.2 mg/kg; mice were killed 1 or 24 h after PEPD dosing,and plasma PEPD level was measured by ELISA along with that in thecontrol mice. Each value is a mean±SD. The result shows that EP helpselevate plasma PEPD level by at least 50 fold.

FIG. 15. Data showing the effects of PEPD and coagulation inhibitor EPin vivo. CHO-K1/ErbB2 cells were inoculated subcutaneously to the flanksof female athymic nude mice (6-7 weeks of age) at 1×10⁶ cells per sitein a small volume of PBS:Matrigel mix. Starting 4 days after cellinoculation, the mice were given either vehicle or enoxaparin (EP) at2.5 mg/kg by intraperitoneal injection once daily. After 3 days of EPtreatment (day 7 after cell inoculation), when tumor volume reachedapproximately 41 mm³, a subset of EP-treated mice were also treated withPEPD at 0.02 mg/kg or 0.2 mg/kg by intraperitoneal injection, which wasgiven three times per week (Monday, Wednesday, Friday). On the days whenboth EP and PEPD were given, PEPD was given 1 h after EP. Tumor volumewas measured three times per week (Monday, Wednesday, Friday). The micewere killed 24 h after the last treatment (on day 24 after cellinoculation, and a total of 8 PEPD treatments), and blood samples werecollected from the mice for measurement of plasma level of PEPD by anELISA assay. (a) Each value is a mean±SEM (n=8-11). (b) Each value ismean±SD (n=3). PEPD strongly inhibited tumor growth but EP had noeffect.

FIG. 16. Data showing the effects of PEPD and coagulation inhibitor EPin vivo. CHO-K1 cells were inoculated subcutaneously to the flanks offemale athymic nude mice (6-7 weeks of age) at 1×10⁶ cells per site in asmall volume of PBS; Matrigel mix. Starting 4 days after cellinoculation, the mice were treated with EP at 2.5 mg/kg byintraperitoneal injection once daily. Three days later (day 7 after cellinoculation), when the tumor volume reached approximately 26 mm³, themice were also treated with vehicle or PEPD at 0.2 mg/kg byintraperitoneal injection, which was given three times per week (Monday,Wednesday, Friday). On the days when both EP and PEPD/vehicle weregiven, PEPD/vehicle was given 1 h after EP. Tumor volume was measuredthree times per week (Monday, Wednesday, Friday). The mice were killed24 h after the last treatment which was given on day 21 after cellinoculation (a total of 7 PEPD treatments), and blood samples werecollected from the mice for measurement of plasma level of PEPD. (a)Each value is a mean±SEM (n=8-11). (b) Each value is mean±SD (n=3). Thisshows that PEPD does not target tumors without ErbB2 overexpression.Notably, these tumor cells do not express ErbB1, ErbB3 or ErbB4, asshown in FIG. 8 a.

FIG. 17. Data showing strong inhibition of orthotopic mammary tumors byPEPD but stronger inhibition of the tumors by enzymatically inactivePEPD (PEPD^(G278D)). Female athymic nude mice (6-7 weeks of age) wereeach implanted subcutaneously (in the back) with a 60 day release of17β-estradiol pellet (1.7 mg of estradiol), prior to orthotopicinoculation of breast cancer BT-474 cells into the mammary fat pads(2×10⁶ cells per site in a small volume of PBS:Matrigel mix). (a) Plotof tumor size over days of growth. EP (0.5 mg/kg) was given daily byintraperitoneal injection. Notably, EP at this dose was as effective as2.5 mg/kg in elevating plasma level of PEPD. EP dosing was alwaysstarted 4 days earlier than PEPD or PEPD^(G278D). PEPD and PEPD^(G278D)were given thrice weekly (Monday, Wednesday, Friday), each at 2 mg/kg byintraperitoneal injection. Each value is a mean±SEM. (b) Graph showingplasma PEPD in view of EP, PEPD and PEPD^(G278D) treatments at day 58 ofgraph shown in panel a; each value is a mean±SD.

FIG. 18. For comparison of PEPD-Fc with PEPD for impact on ErbB2 anddownstream signals, CHO-K1/ErbB2 cells were treated with vehicle,PEPD-Fc (27 nM) or PEPD (27 nM) for 3 or 6 h, followed by western blotanalysis. The human PEPD-human Fc hybrid (Fc linked in frame to thecarboxyl end of PEPD) was prepared by us using standard recombinanttechnology.

FIG. 19. Data summarizing tumor inhibition and molecular changes intumors treated by rhPEPD or rhPEPD^(G278D). rhPEPD or rhPEPD^(G278D) arethe same as PEPD or PEPD^(G278D) or G278D-PEPD described before. Tumorsin several experimental groups shown in FIG. 17 were too small formolecular analysis. (a) Sizes of tumors derived from mammary fat padBT-474 cell xenografts upon treatment with vehicle, EP, EP plus rhPEPDor EP plus rhPEPDG278D. EP: daily at 0.5 mg per kg body weightintraperitoneally, started 4 days before rhPDPD or rhPEPD^(G278D).rhPEPD or rhPEPD^(G278D): 2 mg per kg body weight intraperitoneally,only two doses separated by 2 days. Error bars are s.e.m. (n=3-6). (b)Immunoblots comparing major cell signaling changes in tumor specimensobtained 24 h after the final dose as indicated in a. Each samplerepresents one tumor. (c, d) SRC kinase activity and PI3K activity intumor specimens obtained 24 h after the final dose as indicated in a.Error bars are s.d. (n=3). (e) Immunoblots comparing HIF-1α signalingchanges in tumor specimens obtained 24 h after the final dose asindicated in a. Each sample represents one tumor. As HIF-1α and relatedfactors (vascular endothelial growth factor [VEGF] and glucosetransporter 1 [GLUT-1]) are pro-survival factors, the result explains atleast in part why rhPEPD^(G278D) is a more powerful antitumor agent thanrhPEPD is. The stimulatory effect of rhPEPD on these pro-survivalfactors is believed to depend on its dipeptidase activity. Both rhPEPDand rhPEPD^(G278D) are internalized by tumor cells (measured by theirHis tag, FIG. 19e ) apparently via ErbB2.

DESCRIPTION OF THE DISCLOSURE

The present disclosure is based at least in part on our discoveries thatPEPD is a ligand of the ErbB2 receptor and that it can be used forinhibiting the growth of ErbB2-positive cancers. In particular, andwithout intending to be constrained by any particular theory, wedemonstrate in the present disclosure that PEPD is an ErbB2 ligand whichbinds to subdomain 3 of the ErbB2 extracellular domain. PEPD binds toErbB2 as a homodimer, with each subunit apparently binding to one ErbB2monomer. When PEPD binds to pre-existing ErbB2 dimers, it rapidlysilences the ErbB2-Src/CK2-PTEN-AKT signaling system. PEPD also binds toErbB2 monomers, causing ErbB2 dimerization and tyrosine phosphorylation.However, ErbB2 activation by PEPD is apparently insignificant, becausePEPD soon causes profound ErbB2 depletion due to ErbB2 internalizationand degradation and PEPD selectively inhibits the growth of cellsoverexpressing ErbB2. It is also believed from data presented hereinthat PEPD strikes ErbB2 only when it is present in the extracellularspace and does not involve its enzymatic activity. Thus, the presentdisclosure includes but is not limited to the revelations that PEPD is aligand of the ErbB2 receptor but suppresses ErbB2 signaling; theenzymatic activity of PEPD is not involved in ErbB2 targeting; PEPD actson ErbB2 only when it is present in the extracellular space; and PEPDselectively inhibits cells overexpressing ErbB2. Data presented hereindemonstrate that PEPD and an enzymatically inactive derivative thereofhave effective anti-Erb2+ cancer effects in clinically relevant animalmodes. In particular, data presented herein demonstrates PEPD and anenzymatically inactive variant thereof specifically targets tumorsoverexpressing ErbB2, and suppression of the Erb2+ tumors is confirmedin an orthotopic breast tumor model. Moreover, data presented hereindemonstrate that compositions and methods of this disclosure areeffective in preventing recurrence of at least some Erb2+ tumors aftercessation of treatment with the PEPD formulations.

The amino acid sequence of ErbB2 is provided in GenBank accession no.NM_004448.2. While variants in ErbB2 are known in the art, it isexpected that the present method will function with any ErbB2 variant,provided that the erbB2 variant has an extracellular domain. Theextracellular domain is known in the art and comprises amino acid number23-652 in the primary amino acid sequence in the GenBank accession no.mentioned above.

In more detail, it will be apparent from the instant disclosure and theExamples presented herein that the effect of PEPD on ErbB2 signalingrepresents a novel ligand-induced ErbB2 signaling as well as a novelPEPD function. A non-limiting, graphical illustration of thisrelationship is depicted in FIG. 6 which, without intending to beconstrained by theory, demonstrates how selective inhibition of cellsoverexpressing ErbB2 by PEPD could exhibit therapeutic utility of PEPDagainst ErbB2-positive breast cancers and other cancers in humans.

PEPD is a relatively high-affinity ligand (Kd=7.3 nM, FIG. 1c ), andexerts potent impact on ErbB2 signaling. PEPD binds to subdomain 3 inthe ErbB2 ECD, although the exact residues involved in binding remainundefined. While it was previously indicated that ErbB2 ECD adopts afixed conformation that resembles a ligand-activated state, rendering itready for homo- or hetero-dimerization in the absence of direct ligandbinding (Cho H S, et a. Nature 2003, 421(6924): 756-760), the presentdisclosure indicate that this model is incomplete. PEPD causes atwo-step ErbB2 signaling shutdown. Within minutes of PEPD treatment, thepreassembled signaling complex of ErbB2-Src-CK2 is disrupted. Both Srcand CK2 dissociate from ErbB2 and become inactivated, leading to changesin downstream signals: PTEN dephosphorylation and relocation to cellmembrane, and AKT dephosphorylation (presumably due to PIP3dephosphorylation by PTEN). However, PEPD has no effect on PI3K whichapparently associates with ErbB2 via ErbB3. However, in vivo in thetumor tissues, PEPD as well as PEPD^(G278D) silenced ErbB3 and PI3K(FIG. 19), apparently by disrupting ErbB2-ErbB3 association, which wasnot detected in our in vitro studies due to relatively short PEPDtreatment times. Because the impact of PEPD on Src and CK2 occurs in theabsence of apparent ErbB2 depletion, PEPD binding to ErbB2 dimer likelycauses conformation change of the latter, rendering it unable to holdSrc. PEPD also binds to ErbB2 monomer, causing ErbB2 dimerization andactivation, which occurs somewhat slowly, as peak phosphorylation levelsof ErbB2 and ERK were detected after 3 h of PEPD treatment. However,PEPD-induced ErbB2 activation is likely functionally insignificant, asPEPD also causes profound and sustained depletion of ErbB2, which becameevident after 1-3 h of PEPD treatment and reached maximal depletion at 6h, which was sustained for at least 72 h. PEPD was able to cause almostcomplete ErbB2 depletion (FIG. 2c ). PEPD-induced ErbB2 depletionappears to result entirely from ErbB2 internalization and degradation,as PEPD has no effect on ErbB2 ECD cleavage, nor does it modulate ErbB2gene expression. Thus, the present disclosure reveals a fundamentallydifferent and new function of PEPD. PEPD has been known as a cytosolicdipeptidase. We have now learned that not only PEPD is an ErbB2 ligand,but a PEPD mutant which losses 99.4% of its dipeptidase activity is aseffective as the wild type protein. Moreover, in vivo, the PEPD mutantis more efficacious than PEPD itself in combating ErbB2-driven tumors(FIG. 17). Intracellular PEPD has no effect on ErbB2, but PEPD isreleased from cells as revealed in the present disclosure, and more PEPDis released from damaged tissues and cells.

Compositions comprising PEPD are expected to be useful for prophylaxisand/or therapy of ErbB2-positive breast cancer and other cancers inhumans. Consistent with its ability to rapidly silence theErbB2-Src/CK2-PTEN-AKT signaling pathway, which plays a major role inErbB2-driven breast cancer, and to cause pronounced and persistentdepletion of ErbB2, we show that PEPD significantly inhibits theproliferation, anchorage-independent colony formation andinvasion/migration of cells overexpressing ErbB2, while exerting littleimpact on cells that have minimum ErbB2 expression, and as describedabove and in more detail below, we demonstrate the anti-cancer effectsof PEPD and an enzymatically inactive derivative thereof usingclinically relevant animal models bearing Erb2+ tumors. The inhibitoryimpact of PEPD on ErbB2 stands in stark contrast to the well-knownstimulatory impact of other ErbB ligands on their receptors. The impactof PEPD on ErbB2 signaling and cells overexpressing ErbB2 is reminiscentof that of trastuzumab. Given the high cost of trastuzumab use in theclinic (the current cost is >$1,000 per dose and about $70,000 for afull course of treatment), PEPD has the advantage that it can be massproduced as further described below at a relatively low cost, and istherefore expected in certain embodiments to be a significant and lessexpensive alternative to trastuzumab. In vivo, trastuzumab neither downregulates ErbB2 expression nor inhibits ErbB2 tyrosine phosphorylationin cancer tissues (Gennari et al., Clin Cancer Res, 10, 5650-5655, 2004;Gijsen et al., PLoS Biol, 8, e1000563, 2010); rather, its antitumoractivity depends mainly on antibody-dependent cell-mediated cytoxicity(ADCC) via its Fc domain (Barok et al., Mol Cancer Ther, 6, 2065-2072,2007; Clynes et al., Nature Med, 6, 443-446, 2000). Thus, PEPD or itsmutant may complement trastuzumab and overcome to certain extent theresistance to trastuzumab in patients.

Any PEPD is expected to be suitable for use in the compositions andmethods of the present disclosure. In embodiments, the PEPD is a PEPDproduced by a prokaryote or a eukaryote. In embodiments, the PEPD isprokaryotic in origin. In non-limiting embodiments, the PEPD is producedby Pseudoalteromonas haloplanktis (i.e., a PEPD comprising the aminoacid sequence under GenBank no. AAA99824.1), or Pyrococcus furiosus(i.e., a PEPD comprising the amino acid sequence under GenBank no.WP_011011876.1). A number eukaryotic PEPD amino acid sequences are alsoknown in the art, including a number of mammalian PEPD amino acidsequences. In embodiments, the PEPD has the sequence of a rodent PEPD,i.e., a mouse or rat, or a non-human primate PEPD, such as chimpanzee ora Rhesus macaque. The amino acid sequence of mouse prolidase is providedunder GenBank accession no. NP_032846.2; rat prolidase is provided underNP_001009641.1; Rhesus macaque prolidase is provided under AFJ71215.1;chimpanzee prolidase is provided under NP_001267459.1. The amino acidsequence of human prolidase (PEPD) in SEQ ID NO:1 is known in the art.SEQ ID NO:1 and the cDNA sequence encoding it is accessible via GenBankaccession no. J04605.1; the amino acid sequence is also provided underGenBank accession number AAA60064. In one illustrative but not limitingembodiment, enzymatically active human PEPD has the sequence of SEQ IDNO:1:

(SEQ ID NO: 1) MAAATGPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTDTGVLFLQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEIVESRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYGLESLFEHYCYSRGGMRHSSYTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDM

GEYYSVASDITCSFPRNGKFT ADQKAVYEAVLLSSRAVMGAMKPGDWWPDIDRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVIDSGIELLTCVPRTVEEIEACMAGCDKAFTPFSGPK 

In SEQ ID NO:1, the G at position 278 is shaded, bolded and italicizedand represents the location of a G278D mutation which renders the PEPDenzymatically inactive. In embodiments, the mutation is a change ofglycine at position 278 to an amino acid other than aspartic acid.

All of the amino acid and polynucleotide sequences provided under theGenBank accession numbers referenced in this disclosure are incorporatedherein by reference as those sequences were available through GenBank onthe date of filing of this application. This disclosure also includesall polynucleotides encoding PEPD and all variants of it that aredescribed herein or which would otherwise be known to the skilledartisan given the benefit of the present disclosure.

Rodent (mouse and rat) PEPD amino acid sequences are more than 86%similar to the human sequence, while non-human primate PEPD amino acidsequences, such as the Rhesus macaque, is over 95% similar to the humanPEPD amino acid sequence. In embodiments, the PEPD comprises or consistsof a human PEPD amino acid sequence. In embodiments, the PEPD used inthe compositions and/or methods of the present disclosure is at betweenat least 85.0% and 99.9%, inclusive, and including all numerals to thefirst decimal place there between, similar to the sequence of SEQ IDNO:1. In an embodiment, the PEPD comprises an amino acid sequence thatis at least 95% similar to the sequence of SEQ ID NO:1.

In various embodiments, the present disclosure includes compositionscomprising wild type PEPD (e.g., PEPD of SEQ ID NO:1), or modified PEPD,or a combination thereof. In general, modifications to PEPD suitable foruse with the present invention can be determined by those skilled in theart using ordinary techniques, given the benefit of the presentdescription. In embodiments, modified PEPD comprises modifications ofSEQ ID NO:1. The disclosure includes all modifications of SEQ ID NO:1 solong as the PEPD retains the capability to bind to and cause depletionof ErbB2 from the cell surface. In embodiments, modified PEPD retainsthe capability to form a homodimer. In embodiments, contacting anErbB2-positive cell with a modified (or wild type) PEPD of thisdisclosure is followed by ErbB2 binding and endocytosis of ErbB2,resulting in ErbB2 depletion. Modified PEPD that maintain some or all ofthese functional attributes may comprise amino acid insertions,deletions and substitutions. For example, the disclosure includes PEPDwhich has been modified by conservative amino acid substitutions thatare based generally on relative similarity of R-group substituents.Non-limiting examples of such substitutions include gly or ser for ala;lys for arg; gln or his for asn; glu for asp; ser for cys; asn for gln;asp for glu; ala for gly; asn or gln for his; leu or val for ile; ile orval for leu; arg for lys; leu or tyr for met; thr for ser; tyr for trp;phe for tyr; and ile or leu for val. Thus, a PEPD that comprises anysingle conservative amino acid substitution, or any combination ofconservative amino acid substitutions, are included in the disclosureprovided they can at least retain the capability to bind to ErbB2, withsubsequent depletion of ErbB2 from the cell surface. It will be apparentto those skilled in the art how to determine whether or not anyparticular modified PEPD can bind to ErbB2. In embodiments, the modifiedPEPD can bind the ErbB2 extracellular domain with an estimated Kd valueof 7.3 nM, as determined using an ELISA assay.

Wild type PEPD is enzymatically active. Modified PEPD is a PEPD thatcomprises a change in SEQ ID NO:1 and can be enzymatically active orenzymatically inactive. In this regards, it is known in the art thatdefects in the iminodipeptidase activity of PEPD is associated withPolidase Deficiency, which is a very rare autosomal recessive diseaseassociated with collagen metabolism and affects connective tissues. Thusit is known that the enzymatic activity of PEPD is important. However,in embodiments, enzymatically inactive PEPD is used in the compositionsand methods of this disclosure. Enzymatically inactive PEPD isconsidered to be a PEPD that exhibits less hydrolysis of a substratedipeptide that has proline or hydroxyproline at its carboxy terminusthan the amount of such hydrolysis exhibited by a reference proteinwhich comprises or consists of the sequence of SEQ ID NO:1. Inembodiments, enzymatically inactive PEPD can have at least between0.0%-99.9%, inclusive, and including all digits there between to thefirst decimal point, less dipeptide hydrolysis activity as compared to areference PEPD. In one embodiment, an enzymatically inactive PEPD has nomore than 0.6% dipeptide hydrolysis activity of a reference PEPD. In oneembodiment, the reference PEPD comprises or consists of the sequence ofSEQ ID NO:1. One unit of prolidase activity can be defined as the amountof enzyme that releases 1 μmol of proline/h under standard assayconditions. In one embodiment, an enzymatically inactive PEPD has nodetectable PEPD dipeptide hydrolysis activity. In an embodiment, anenzymatically inactive PEPD comprises a G278D mutation. In embodiments,the disclosure includes any one, or any combination of PEPD mutationsdisclosed herein, and accordingly includes the proviso that any singleor any combination of such mutants can be excluded from the invention.

PEPD used in embodiments of this disclosure can include modificationsthat enhance its desirable characteristics, such as the capability tobind to or enter a tumor cell or tumor microenvironment, or to enhancecirculation time, bioavailability, stability, or uses related toErbB2-positive cell-targeted killing, or ErbB2-positive cell imaging.PEPD proteins that can be used with the present disclosure include apolypeptide comprising SEQ ID NO:1 or a modification thereof, and inembodiments also include such PEPD polypeptides within the context of alarger polypeptide. Modifications to SEQ ID NO:1 include modificationsthat abrogate or lessen enzymatic activity, and/or changes that do notaffect the capability of the modified PEPD to bind to ErbB2. Thus, thePEPD of SEQ ID NO:1 can be modified by conservative amino acidsubstitutions that are based generally on relative similarity of R-groupsubstituents. Non-limiting examples of such substitutions contemplatedinclude, but are not limited to: gly or ser for ala; lys for arg; gln orhis for asn; glu for asp; ser for cys; asn for gln; asp for glu; ala forgly; asn or gln for his; leu or val for ile; ile or val for leu; arg forlys; leu or tyr for met; thr for ser; tyr for trp; phe for tyr; and ileor leu for val. Thus, PEPDs that comprise any single conservative aminoacid substitution, or any combination of conservative amino acidsubstitutions, are included in this disclosure, so long as they retaintheir ErbB2-binding properties, and can inhibit growth of ErbB2-positivecells. Thus, the instant disclosure includes polypeptide sequences thatcomprise SEQ ID NO:1 or modifications thereof, and can include furthermodifications, including but not necessarily limited to additional aminoacids, and/or by being provided as part a complex with othercompositions of matter. Thus, the PEPD polypeptides could be part oflarger proteins, such as fusion proteins, or they could be connected toother moieties. Accordingly, the PEPD proteins could be covalently ornon-covalently associated with any desirable moiety that would beexpected to improve their functional capabilities in accordance with theprophylaxis and/or therapy of ErbB2-positive cancers.

In general, the PEPD protein (and if desired a polypeptide sequence withwhich it is made as a single fusion protein) can be made usingconventional techniques. For example, in embodiments, PEPDprotein/fusion protein can be made using prokaryotic or eukaryoticexpression systems. Thus, the disclosure provides manufacturingadvantages over other ErbB2 binding partners, such as mAbs directed atErbB2, which are expensive and time consuming to make. For recombinantproduction of proteins comprising or consisting of a PEPD as describedherein, in general, any polynucleotide encoding the PEPD can be providedin an expression vector. “Expression vector” refers to a vectorcomprising protein expression control sequences operatively linked tothe PEPD coding sequence. The expression vector can comprise cis-actingelements for expression, including but not limited to promoter elements,enhancer elements, origins of replication, selectable markers,transcription initiation sites, sequences that encode translationinitiation sites, and any other sequence that is desirable for proteinexpression, depending on the expression system chosen. Suitable proteinexpression vectors which can be designed to express any polynucleotidesequence encoding PEPD (each of which PEPD-encoding sequences isencompassed within this disclosure) include all those known in the art,examples of which include but are not limited to cosmids, plasmids andvirus-based systems that incorporate the recombinant polynucleotideencoding the PEPD. The system used to express the recombinant PEPDproteins of the invention can be any suitable organism and include butare not limited to mammalian cell expression systems, insect cellexpression systems (e.g., baculovirus-based systems), yeast expressionsystems, plant cell expression systems, and prokaryotic expressionsystems. In one embodiment, E. coli is used for PEPD expression. In oneembodiment, a PEPD chimeric protein is expressed recombinantly using amammalian expression system so that the chimeric protein compriseshuman-specific glycosylation.

In an embodiment, a PEPD protein can be conjugated to an immunoglobulin(Ig) or a fragment thereof to provide a chimeric PEPD/Ig molecule. Sucha construct is expected to be useful in involving various aspects of theimmune response of the individual to facilitate targeted killing ofErbB2+ cells. The immunoglobulin or fragment thereof can be any Ig typeor subtype. In this regard, previous studies have indicated thatantibody-dependent cellular cytotoxicity (mediated via Fc receptors)plays a critical part in trastuzumab targeting of ErbB2-positive breastcancer (Clynes et al., Nature Med, 6, 443-446, 2000; Spiridon et al.,Clin Cancer Res, 10, 3542-3551, 2004). The present disclosure likewiseencompasses PEPD-Fc chimeric proteins and pharmaceutical compositionscomprising them. Methods for making Fc-chimeric proteins are known inthe art. For example, pFUSE-Fc vectors, commercially available fromInvivoGene, can be used to generate PEPD-Fc fusion hybrids. Thus, in oneembodiments the disclosure includes a composition comprising a fusionprotein, wherein the PEPD in a component of the fusion protein, andwherein the fusion protein comprises an Fc region of a human Ig. Invarious embodiments, the Fc region is an Fc region or fragments thereofis from an IgA, IgG, or IgE antibody, although Fc regions from otherantibody types, or synthetic/artificial Fc regions can also be used. Inembodiments, the Fc region is a human IgG2a or human IgG1 or a fragmentof such Fc regions. The Fc region can comprise or consist of an aminoacid sequence that is identical to an Fc region produced by a mammal,such as a human. In various embodiments, the Fc region may have between80% to 100% (including all integers there between) amino acid sequencesimilarity to an Fc region produced by a mouse and/or a human. The Fcregion may be an intact Fc region, meaning an entire Fc region, or maybe a fragment of the Fc region. Those skilled in the art will recognizethat the “Fc region” of an antibody means the “Fragment, crystallizable”region of the antibody, which comprises two heavy chains that contributetwo or three constant domains (CD) depending on the class of theantibody. Nucleotide sequences encoding Fc regions, as well as the aminoacid sequences of Fc regions for mouse and human immunoglobulins arewell known in the art. In one embodiment, the Fc portion of the fusionproteins comprises only antibody heavy chain(s). Those skilled in theart will recognize that for demonstration of the invention using murineanimal models, the Fc portion of the fusion protein may be an IgG2a orIgG2b Fc murine Ig portion, while for therapy and/or prophylaxis ofdisease in humans, the Fc portion is preferably an IgG1 or an IgG3 Fcportion. In certain embodiments, the Fc portion of the fusion proteinsprovided herein do not include antigen recognition portions (i.e., theantibody portion of the fusion proteins do not contain antibody variableregions). Thus, the fusion proteins are distinct from antibodies that docontain antigen binding portions. DNA constructs encoding the Fc-fusionPEPD proteins can be made using any conventional techniques well knownto those skilled in the art. For example, the Fc-fusion encodingconstructs can be made using commercially available reagents. Forinstance, INVIVOGEN offers the pFUSE-Fc family of plasmids developed tofacilitate the construction of Fc-Fusion proteins by fusing a sequenceencoding a given protein to the Fc region of an immunoglobulin (Ig). Inthis construct, the Fc region comprises the CH2 and CH3 domains of theIgG heavy chain and the hinge region. The hinge acts as a flexiblespacer between the two parts of the Fc-fusion protein, which permitseach part of the fusion protein to function independently if desired.

As described above, the disclosure includes any PEPD protein as acomponent of a fusion protein which can include any other amino acidsequence that would be desirable for expressing in the same open readingframe as the PEPD protein, and can include but are not limited to aminoacid sequences involved in facilitating protein isolation and/orpurification, for solubility, secretion, or any other function. The PEPDpolypeptide can be configured N-terminal or C-terminal to the fused openreading frame, depending on the particular fusion protein to beproduced. For example, the PEPD proteins can be provided with ahistidine tag, such as a suitable polyhistidine tag. In embodiments, thehistidine tag comprises at least six histidines in sequence. In anembodiment, the his tag is a hexa-histidine peptide sequence. In anembodiment, if desired, a PEPD expression system can be configured sothat the histidine tag can be removed, such as by including a tobaccoetch virus (TEV)-cleavable, N-terminal hexa-histidine tag.

In non-limiting embodiments, the PEPD polypeptides can be combined withor coupled to a chemotherapeutic agent, or any other agent that hascytotoxic activity, or agents that are useful for detection and/orimaging of ErbB2-positive cells/tissues. For example, PEPD conjugatesmay include enzymatically active toxins and fragments thereof or smallmolecules. Suitable enzymatically active toxins and small moleculesinclude but not limited to docetaxel, mitoxanthrone, taxanes, diphtheriaA chain, nonbinding active fragments of diphtheria toxin, exotoxin Achain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain,modeccin A chain, alpha sarcin, Aleurites fordii proteins, dianthinproteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S),momordica charantia inhibitor, curcin, crotin, sapaonaria officinalisinhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin andthe tricothecenes, microtubule-targeting agents, or any anti-angiogenicagent(s).

Conjugates and combinations of the PEPD protein and chemotherapeuticagents (or other agents, such as imaging agents) may be made using anysuitable techniques. In various embodiments, the PEPD protein can beproduced separately from the chemotherapeutic agent, and then chemicallycoupled to it, or in the case of protein agents, the PEPD protein can beproduced as a PEPD/protein fusion to yield a novel chimeric protein. Forchemical coupling, a variety of bifunctional protein coupling agentssuch as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP),succinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate,iminothiolane (IT), bifunctional derivatives of imidoesters (such asdimethyl adipimidate HCL), active esters (such as disuccinimidylsuberate), aldehydes (such as glutareldehyde), bis-azido compounds (suchas bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (suchas bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene) can be used to covalently join a PEPDand a chemotherapeutic or other agent, such as an imaging agent.

In another embodiment, the PEPD can be conjugated to a radioactiveagent. A variety of radioactive isotopes are available for conjugatingto proteins such that ErbB2-positive cells or tissues to which the PEPDbind can be imaged or selectively destroyed. For selective destructionof cells the peptides can be conjugated to a highly radioactive atom,such as At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, Pb212and radioactive isotopes of Lu. For identifying ErbB2-positive cells,the PEPD conjugates can include a radioactive atom for scintigraphicstudies, for example Tc99m (metastable technetium-99), I123, or a spinlabel for nuclear magnetic resonance and/or magnetic resonance imaging,such as I123, I131, In111, F19, C13, N15, O17 or Gadlinium (III) orManganese (II). The radio-labels may be incorporated in the PEPDproteins in known ways.

The PEPD proteins can be provided in pharmaceutical compositions foradministration by combining them with any suitable pharmaceuticallyacceptable carriers, excipients and/or stabilizers. Some suitableexamples of pharmaceutically acceptable carriers, excipients andstabilizer can be found in Remington: The Science and Practice ofPharmacy (2005) 21st Edition, Philadelphia, Pa. Lippincott Williams &Wilkins. Further, any suitable delivery vehicle can be used in theinvention, such as a controlled release delivery formulation in whichthe PEPD is released over a period of time. If desired, thepharmaceutical composition can comprise both PEPD and a coagulationinhibitor.

Administration of formulations comprising PEPD as described herein canbe performed using any suitable route of administration, including butnot limited to parenteral, intraperitoneal, intrapulmonary, oral, andintra-tumoral. Parenteral infusions include intramuscular, intravenous,intraarterial, intraperitoneal, and subcutaneous administration.

The amount PEPD and any other active agent to be included in acomposition and/or to be used in the method can be determined by thoseskilled in the art, given the benefit of the present disclosure. Thus,in one embodiment, an effective amount of a composition of the inventionis administered. An effective amount can be an amount of the compositionthat inhibits growth of cells in the individual that express ErbB2, oran amount that extends the survival of the individual, or thatalleviates disease symptoms associated with expression of the ErbB2 inthe individual, or suppresses a malignant phenotype of cellsoverexpressing ErbB2. In embodiments, the individual to whom acomposition of the invention is administered has, is suspected ofhaving, or is at risk for development and/or recurrence of anErbB2-positive cancer. In embodiments, the ErbB2-positive cancer is abreast cancer, bladder cancer, ovarian cancer, stomach cancer, oraggressive forms of uterine cancer, such as uterine serous endometrialcarcinoma, or other cancers overexpressing ErbB2, or cancers whose stemcells overexpress ErbB2, or metastatic cancers overexpressing ErbB2.

Suitable dosages for either therapeutic or prophylactic purposes can bedetermined by those skilled in the art and will be based, at least inpart, on consideration of the individual's age, sex, size, and health,the type of delivery system used, the stage of disease, and otherfactors as will be apparent to the skilled artisan. In embodiments, PEPDdosing for human subjects may be similar to or the same as dosing fortrastuzumab, which is typically 2-4 mg/kg weekly.

Compositions of the disclosure can be administered in conjunction withany conventional treatment regimen, including sequential or simultaneousadministration of chemotherapeutic agents, passive immunotherapies,vaccines, adjuvants, the like. In particular embodiments, the method canbe performed in conjunction with conventional therapies that areintended to treat a disease or disorder associated with ErbB2-positivecells. For example, administration of compositions described herein canbe combined with treatment modalities including but not limited tochemotherapies, surgical interventions, and radiation therapy which canbe performed prior to, concurrently, or subsequent to PEPDadministrations. In embodiments, the disclosure includes a compositioncomprising PEPD and cetuximab, a clinically used monoclonal antibodyagainst ErbB1. In embodiments, the disclosure includes a compositioncomprising PEPD with the clinically used dual ErbB1/ErbB2 kinaseinhibitor lapatinib. In embodiments, the disclosure includescompositions comprising PEPD and trastuzumab. In embodiments, thedisclosure includes compositions comprising PEPD and pertuzumab, anotherclinically used anti-ErbB2 monoclonal antibody.

In embodiments, the disclosure includes compositions and methods forusing the compositions, wherein in addition to a PEPD protein, thecompositions comprise a blood coagulation inhibitor. In one embodiment,the coagulation inhibitor is an agent that inhibits PEPDs degradation invivo, so as to reduce PEPD dose required by patients. In one embodiment,the coagulation inhibitor inhibits conversion of prothrombin tothrombin, or inhibits the participation of thrombin in clot formation.In an embodiment, the coagulation inhibitor interferes with the clottingrelated function of the clot-promoting proteins known as factor X andfactor II. In embodiments, the coagulation inhibitor binds to andactivates antithrombin III, and as a consequence, coagulation factors Xaand IIa are inhibited. In an embodiment, the coagulation inhibitor isheparin, such as an unfractionated heparin preparation, or a lowmolecular weight form of heparin. Low molecular weight forms of heparinare known in the art (i.e., Weitz J I; Weitz, Jeffrey I. (1997).“Low-molecular-weight heparins”. N Engl J Med 337 (10): 688-98). In anembodiment, the low molecular weight heparin is enoxaparin or apharmaceutically acceptable salt thereof, such as enoxaparin sodium. Inan embodiment, the inhibitor is a direct Xa inhibitor, either oral ornon-oral, including but not limited to the drugs sold under the tradenames RIVAROXABAN, APIXABAN or EDOXABAN. In an embodiment, thecoagulation inhibitor may be an inhibitor of other blood coagulationfactors, including but not limited to Factors XII, XI and VII. Inembodiments, the low molecular weight heparin or other coagulationinhibitor is administered using any suitable vehicle and route ofadministration. In embodiments, the coagulation inhibitor isadministered by subcutaneous injection. In one embodiment, thecoagulation inhibitor is administered orally. The dose of thecoagulation inhibitor can be based on the individual recipient's weightand other parameters that will be recognized by those skilled in the artgiven the benefit of this disclosure. In embodiments, the coagulationinhibitor can be given prior to, concurrent with, or subsequent to thePEPD composition, and may be administered with the same number andtiming of the PEPD administration(s), or may be administered accordingto a schedule that is different than the PEPD administration.

In another embodiment, the present disclosure provides a method foridentifying whether an individual is a candidate for treatment with acomposition comprising a PEPD. The method comprises obtaining abiological sample from the individual and determining whether the samplecomprises ErbB2-positive cancer cells, wherein determining that thebiological sample comprises ErbB2-positive cancer cells is indicativethat the individual is a candidate for the treatment, and whereindetermining that the biological sample does not comprise ErbB2-positivecancer cells is indicative that the individual is not a candidate forthe treatment. Thus, in embodiments, the present disclosure provides foraiding in the diagnosis, or for diagnosing an individual as in need oftreatment with a composition comprising a PEPD. In embodiments, themethod comprises communicating a determination of presence or absence ofErbB2-positive cancer cells in the biological sample to a health careprovider so that the health care provider can, in one embodiment,recommend treatment with a composition comprising a PEPD. Inembodiments, the method further comprises administering a compositioncomprising a PEPD to the individual. A determination of the presence ofErbB2-positive cancer cells comprises detecting in an individual or abiological sample obtained from the individual's cancer cells whichoverexpress ErbB2.

In an embodiment, the method of identifying whether an individual is acandidate for treatment with a composition comprising a PEPD comprisesobtaining a biological sample from the individual and determiningwhether the sample comprises ErbB2-positive cancer cells and/oroverexpresses ErbB2 by contacting the sample with a detectably labeledPEPD. Detecting a complex of ErbB2+ and detectably labeled PEPD isindicative that the individual is a candidate for treatment with acomposition comprising PEPD as described herein. In an embodiment, thecomplex of ErbB2+ and detectably labeled PEPD is detected on a biopsy ofa tumor that is suspected of comprising ErbB2-positive cells. Inalternative embodiments, PEPD bound to an ErbB2-positive cell can bedetected by using a detectably labeled PEPD binding partner. Inembodiments, ErbB2-positive cancer cells express more ErbB2 than areference. The reference can be any suitable reference, such as amatched control, a standardized value (i.e., area under a curve), and/orvalues for ErbB2 amounts expressed by a cell of the same tissue type ina sample, wherein the ErbB2 cells are not cancer cells. In general, incertain embodiments, identification of a human subject as a candidatefor treatment with a PEPD formulation is performed using the same orsimilar criteria as for identifying an individual as a candidate fortherapy with trastuzumab, which is based on clinically establishedparameters and will be known to the skilled artisan. For example,immunohistochemistry (IHC) is frequently used to measure the amount ofErbB2 present in a tumor biopsy sample, or alternatively fluorescence insitu hybridization (FISH) is used to measure the number of copies of thegene (see, for example, Carlson R W et al., J Natl Compr Canc Netw 2006,Suppl 4, S1-22; Her2 testing in breast cancer: NCCN Task Force reportand recommendations.). In embodiments, a tumor with an IHC score of 0 or1+, an average ErbB2 gene/chromosome 17 ratio of less than 1.8, or anaverage number of ErbB2 gene copies/cell of 4 or less as determined byFISH is considered to be ErbB2 negative. A tumor sample with an IHCscore of 3+, an average ErbB2 gene/chromosome 17 ratio of greater than2.2 by FISH, or an average number of ErbB2 gene copies/cell of 6 orgreater is considered ErbB2 positive within the context of identifyingindividuals who are candidates for cancer therapy using agents thattarget ErbB2.

In embodiments the disclosure further provides products, e.g. articlesof manufacture, which comprise PEPD pharmaceutical preparations. Theproducts comprise isolated and/or purified PEPD. The PEPD can be anenzymatically active or inactive form of PEPD. The articles ofmanufacture include packaging and/or printed material. In oneembodiment, the instant disclosure includes a closed or sealed packagethat contains a PEPD preparation. In certain embodiments, the packagecan comprise one or more closed or sealed vials, bottles, blister(bubble) packs, or any other suitable packaging for the sale, ordistribution, or use of the PEPD pharmaceutical agents. The printedmaterial can include printed information. The printed information can beprovided on a label, or on a paper insert, or printed on the packagingmaterial itself. The printed information can include information thatidentifies the PEPD agent in the package, the amounts and types of otheractive and/or inactive ingredients, and instructions for taking thecomposition, such as the number of doses to take over a given period oftime, and/or information directed to a pharmacist and/or another healthcare provider, such as a physician, or a patient. The kit can compriseand the printed information can identify an additional agent, such as acoagulation inhibitor, that is provided separately or in combinationwith the PEPD agent. The printed material can include an indication thatthe PEPD pharmaceutical composition and/or any other agent provided withthe kit is for the treatment of an ErbB2-positive cancer. The productcan be provided as a kit comprising a therapeutically effective amountof a PEPD composition, packaged in a container, the kit furthercomprising a label attached to or packaged with the container, the labeldescribing the contents of the container and providing indicationsand/or instructions regarding use of the contents of the container totreat ErbB2-positive cancer.

The following Examples are intended to illustrate but not limit theinvention.

Example 1

This Example demonstrates that human PEPD binds to subdomain 3 in thehuman ErbB2 ECD and causes ErbB2 dimerization.

Recombinant human PEPD was generated in bacteria as described furtherbelow and was incubated at 0.04, 0.2 or 1 μM with 0.04 μM ofErbB2/ECD-Fc [a recombinant chimera of human ErbB2 ECD (Thr23-Thr652)and the Fc fragment of human IgG₁] or 0.04 μM of Fc as a control. PEPDbound specifically to the ECD, and each PEPD subunit bound maximally toone copy of ECD (FIG. 1a ). Given that both PEPD and ErbB2/ECD-Fc (dueto Fc) form homodimers in solution, the above result indicates that onePEPD dimer binds to one ECD dimer. PEPD was also incubated at 1 μM with0.04 μM of ErbB3/ECD-Fc [a chimera of the ECD (Ser20-Thr643) of humanErbB3 and Fc] or 0.04 μM of ErbB4/ECD-Fc [a chimera of the ECD(Gln26-Arg649) of human ErbB4 and the Fc], but no binding could bedetected (FIG. 1a ). As expected, neuregulin-1 (NRG-1) bound to the ECDsof ErbB3 and ErbB4 (FIG. 7). Thus, PEPD is not a ligand of ErbB3 orErbB4. We further studied PEPD binding to ErbB2 using Chinese hamsterovary CHO-K1 cells, which expressed a low level of ErbB2 but none of theother ErbBs (FIG. 8a ). Overexpression of human ErbB2 in CHO-K1 cellswas readily achieved by gene transfection (FIG. 1b ). In anenzyme-linked immunosorbent assay (ELISA) using the lysates ofErbB2-overexpressing cells, PEPD bound to ErbB2 with an estimated Kdvalue of 7.3 nM, whereas there was little PEPD binding to the lysates ofcontrol CHO-K1 cells (FIG. 1c ). PEPD did not bind to the trans-membraneand intracellular regions of ErbB2 (FIG. 8b ). Next, we removed the fourECD subdomains of human ErbB2 one at a time (FIG. 1d ), using theErbB2-expressing plasmid pCMV6-XL5-ERBB2 as a template. Similar proteinexpression levels of ErbB2 and its mutants were detected in CHO-K1 cellstransiently transfected with the plasmids (FIG. 1d ). An equal amount ofErbB2 and its mutants, based on western blot quantification, were usedin the same ELISA mentioned above. Subdomain D1 deletion had littleimpact on PEPD-ErbB2 binding; the binding affinity after removingsubdomains D2 and D4 was reduced 3.5 fold and 51.0 fold, respectively,but full PEPD binding was achieved by raising the PEPD concentration;removing subdomain D3 completely abolished PEPD binding (FIG. 1e ).Thus, PEPD bound to D3, but D2 and D4, the latter in particular, mayfacilitate PEPD binding to ErbB2.

Overexpression of ErbB2 in cell is known to cause spontaneousdimerization. As expected, both monomers and dimers of ErbB2 existed inCHO-K1 cells stably overexpressing ErbB2 (FIG. 1f ). Cells were treatedwith cross-linker bis(sulfosuccinimidyl)suberate (BS3) before harvestand western blot analysis. PEPD apparently underwent two phases of ErbB2binding: rapid binding of PEPD homodimers to preexisting ErbB2homodimers (no change in ErbB2 monomer level, decrease in ErbB2 dimerlevel and formation of heterotetramer of 2 ErbB2s and 2 PEPDs at 10 minof PEPD treatment), followed by binding of PEPD homodimer to ErbB2monomer, which was apparent at 30 min of PEPD treatment (decrease inErbB2 monomer level, formation of heterotrimer of 1 ErbB2 and 2 PEPDs,formation of new ErbB2 homodimer, and further increase in heterotetramerof 2 ErbB2s and 2 PEPDs) (FIG. 1f ). Notably, presence of ErbB2homodimers not linked to PEPD after PEPD treatment likely resulted fromincomplete cross-linking of the two proteins by BS3.

Example 2

This Example demonstrates that PEPD induces ErbB2 phosphorylation slowlyand transiently, but causes pronounced and persistent ErbB2 depletion.In CHO-K1/ErbB2 cells which stably overexpressed human ErbB2 and humanbreast cancer BT-474 cells which constitutively overexpressed ErbB2, twokey tyrosine phosphorylation sites on ErbB2, pY1221/1222 and pY1196,were measured. ErbB2 tyrosine phosphorylation at both sites wasevidently increased after 0.5-1 h of PEPD treatment at 2.7 nM, peaked at3 h, and largely returned to basal level at 24 h (FIGS. 2a and 2b ). Athigher PEPD concentrations (27 and 270 nM), ErbB2 tyrosinephosphorylation at these sites increased further and lasted longer (FIG.2c ). The relatively slow ErbB2 tyrosine phosphorylation induced by PEPDis consistent with the relatively slow PEPD binding to ErbB2 monomer andsubsequent dimerization (FIG. 1f ). PEPD binds to preexisting ErbB2dimer rapidly (FIG. 1f ), but it is known that such dimers areauto-tyrosine phosphorylated. As expected, neither epidermal growthfactor (EGF) nor NRG-1 (ligands of other ErbBs) activated ErbB2 inCHO-K1/ErbB2 cells (FIG. 9). In cells treated with PEPD at 2.7 nM, ErbB2protein level began to decrease at 1 h, reached its lowest level at 6 h,which was sustained for at least 72 h (FIG. 2a ), whereas there was nochange in ErbB2 level in vehicle-treated cells (FIG. 2b ). The impact ofPEPD on ErbB2 protein level was dose-dependent, and at 270 nM, PEPDcaused almost total ErbB2 elimination (FIG. 2c ). To understand how PEPDcaused ErbB2 depletion, we measured ErbB2 ECD in the culture medium andErbB2-p95 (minus ECD) in the cell lysates after CHO-K1/ErbB2 cells weretreated with PEPD, since ErbB2 can undergo ECD shedding.4-Aminophenylmercuric acid (APMA) is known to cause ErbB2 ECD cleavageand, as expected, generated the p95 fragment (minus ECD) in the celllysates and the ECD in the medium (FIG. 2d ). However, even when cellswere treated with PEPD at 270 nM for up to 6 h, no ErbB2 ECD sheddingoccurred (FIG. 2d ). Thus, PEPD does not cause ErbB2 ECD cleavage. Also,there was no change in ErbB2 mRNA level in either CHO-K1/ErbB2 cells orBT-474 cells after PEPD treatment for 6 h (FIG. 2e ), indicating thatPEPD-induced ErbB2 depletion was not due to inhibition of ERBB2 geneexpression either. Next, both CHO-K1 cells and CHO-K1/ErbB2 cells weretreated with vehicle or PEPD, followed by immunofluorescence staining ofErbB2 and PEPD and detection by confocal microscopy. Cells were treatedby PEPD at a high concentration (270 nM) to enhance detection. In CHO-K1cells, ErbB2 staining was negligible and there was no PEPD staining(FIG. 2f ), consistent with very low ErbB2 expression in these cells. InCHO-K1/ErbB2 cells, ErbB2 was strongly stained in the plasma membrane,and after incubation with PEPD for 0.25 h, strong PEPD staining in theplasma membrane was also detected, which co-localized with ErbB2 (FIG.2f ), consistent with PEPD binding to ErbB2. However, in CHO-K1/ErbB2cells treated with PEPD for 2 h, staining intensity of both proteins inthe plasma membrane decreased, with concurrent increase of staining inthe cytoplasm (FIG. 2f ), suggesting that ErbB2 and PEPD wereinternalized. ErbB2 was previously shown to undergo clathrin-independentendocytosis, ubiquitination and degradation. Indeed, when cells weretreated with PEPD at 2.7 nM for 0.5 h, level of ubiquitinated ErbB2increased significantly (FIG. 2g ).

Example 3

This Example demonstrates that ErbB2 phosphorylation results from directPEPD binding, but the dipeptidase function of PEPD is not involved. Weanalyzed whether stimulation of ErbB2 phosphorylation by PEPD resultsfrom direct interaction between the two proteins. First, CHO-K1 cellswere transfected with a kinase-dead ErbB2 mutant (K753M) for 24 h andthen treated with PEPD at 270 nM for 3 h, a condition shown to causemaximal phosphorylation of wild-type ErbB2. The ErbB2 mutant wasoverexpressed in the cells after gene transfection, but PEPD failed tostimulate its phosphorylation, whereas under the same experimentalcondition, PEPD stimulated the phosphorylation of the wild-type ErbB2(FIG. 3a ). Next, CHO-K1 cells were transfected with the ErbB2 mutantslacking an ECD subdomain (FIG. 1d ) for 24 h and then treated with PEPDat 270 nM for 3 h. PEPD-induced ErbB2 phosphorylation at bothpY1221/1222 and pY1196 in both ErbB2/delD1 and ErbB2/delD2 wascomparable to that in WT-ErbB2, absent in ErbB2/delD3, and attenuated inErbB2/delD4 (FIG. 3a ), which correlated well with PEPD binding to thesemutants (FIG. 1e ). These results suggest that ErbB2 activation by PEPDin cells results entirely from direct binding of PEPD to ErbB2.

Four mutants of human PEPD were generated and evaluated to betterunderstand PEPD as an ErbB2 ligand, including R184X-PEPD (deletion of309 amino acids from the C-terminus), R265X-PEPD (deletion of 228 aminoacids from the C-terminus), G278D-PEPD (G→D at amino acid #278), andX265R-PEPD (deletion of 228 amino acids from the N-terminus) (FIG. 10a). CHO-K1 cells were transfected with wild-type human ErbB2 for 24 h andthen treated with wild-type PEPD and each of its mutants at 270 nM for 3h. The PEPD mutants failed to induce ErbB2 phosphorylation, exceptG278D-PEPD which was identical to WT-PEPD in activating ErbB2 (FIG. 3b). However, G278D-PEPD is enzymatically inactive (see, e.g., Ledoux P,et al. Expression and molecular analysis of mutations in prolidasedeficiency. Am J Hum Genet 1996; 59: 1035-1039.) Interestingly, onlyWT-PEPD and G278D-PEPD could form homodimers (FIG. 10b ). Thus, thedipeptidase activity of PEPD is not involved in ErbB2 activation, buthomodimerization of PEPD likely is required for PEPD to bind andactivate ErbB2.

Notably, in the experiments described above, PEPD or its G278D mutantdid not cause decrease in ErbB2 protein level, whereas PEPD causedpronounced ErbB2 depletion in cells stably or constitutivelyoverexpressing ErbB2 (FIGS. 2a and 2c ). We found that in CHO-K1 cellstransiently overexpressing ErbB2, the majority of ErbB2 moleculesresided intracellularly, whereas in CHO-K1 cells stably overexpressingErbB2, the majority of ErbB2 molecules were expressed on cell surface(FIG. 11). This may explain why PEPD treatment for 3 h did not cause aclear ErbB2 protein decrease in cells transiently overexpressing ErbB2.

Example 4

This Example demonstrates that intracellular PEPD does not modulateErbB2. PEPD is mainly a cytosolic protein. Endogenous PEPD levels inCHO-K1/ErbB2 cells and BT-474 cells were relatively low, but PEPD levelcould be readily elevated in these cells via gene transfection. Modestor strong PEPD overexpression was detected at 24 h after transfection ofa plasmid expressing human PEPD, but neither ErbB2 tyrosinephosphorylation nor ErbB2 protein expression changed following PEPDoverexpression (FIG. 4a ). To find out whether cells release PEPD,PEPD-overexpressing cells and control cells were cultured in medium for24 h, followed by measurement of PEPD level in the cell lysates bywestern blotting and in the media by ELISA. PEPD concentrations in themedia of PEPD-overexpressing cells were 5.9 fold (CHO-K1/ErbB2 cells)and 10.3 fold (BT-474 cells) higher than in the media of the controlcells (FIG. 4b ). Because all cells appeared morphologically normal andhealthy, the above result suggests that PEPD may be actively released bythe cells. However, due to apparently excessive dilution by the culturemedium, extracellular PEPD concentration was too low (<0.3 nM) to impactErbB2 (FIG. 4b ).

Example 5

This Example demonstrates that PEPD rapidly silences ErbB2-Srcsignaling. ERK lies downstream of ErbB2. As expected, PEPD treatment(2.7 nM) led to ERK activation in a time frame which coincided with thatof ErbB2 phosphorylation (compare FIG. 5a with FIG. 2a ), suggestingrapid signal transmission from activated ErbB2 to ERK. Indeed, in CHO-K1cells expressing the kinase-dead ErbB2 mutant K753M, PEPD caused neitherErbB2 phosphorylation (FIG. 3a ) nor ERK phosphorylation (FIG. 12). AKTalso lies downstream of ErbB2, but its S473 phosphorylation, which iscritical for its function, was reduced by PEPD (2.7 nM) in bothCHO-K1/ErbB2 cells and BT-474 cells in a time-dependent manner (FIG. 5a), whereas vehicle treatment had no impact on AKT phosphorylation (FIG.5b ). This suggested that PEPD modulated ErbB2 signaling via additionalmechanisms. As mentioned before, ErbB2 overexpression causes spontaneousdimerization and auto-tyrosine phosphorylation. It is also known thatSrc and PI3K are activated when bound to tyrosine-phosphorylated ErbB2homodimers or heterodimers, which lead to activation of AKT. InCHO-K1/ErbB2 cells, ErbB2 associated with Src along with CK2, a Srcsubstrate and a pleiotropic serine/threonine protein kinase, but PI3Kwas not detected, whereas in BT-474 cells, ErbB2 associated with Src,CK2 and PI3K (FIG. 5c ). Treatment of these cells with PEPD (2.7 nM) foronly 0.5 h led to marked dissociation of Src and CK2 from ErbB2, butPI3K remained associated with ErbB2 (FIG. 5c ). Accordingly, Src kinaseactivity was significantly attenuated by PEPD in both CHO-K1/ErbB2 cellsand BT-474 cells, while PI3K activity remained unchanged (FIG. 5d ).However, neither Src nor PI3K was significantly modulated by PEPD inCHO-K1 cells (FIG. 5d ). Further experiments showed that Srcphosphorylation at Y419, critical for its kinase function, decreasedsignificantly in both CHO-K1/ErbB2 cells and BT-474 cells aftertreatment with PEPD (2.7 nM) for only 10 min (FIG. 5e ), indicatingrapid PEPD binding to ErbB2 dimers and rapid disruption of the ErbB2-Srcsignaling unit. Given that the impact of PEPD on Src occurred before aclear change in ErbB2 phosphorylation and expression, particularly inCHO-K1/ErbB2 cells (FIG. 2a ), PEPD likely altered the conformation ofpreexisting ErbB2 dimers, causing Src disassociation from ErbB2.

PEPD-induced suppression of Src and CK2 was accompanied by loss of PTENphosphorylation at S380 (FIG. 5a ), compared to vehicle-treated controls(FIG. 5b ). PTEN phosphorylation at this site by CK2 is known tocontribute to the inhibition of PTEN activity. It is also known thatPTEN dephosphorylates membrane-bound PIP3, thereby inhibiting AKTphosphorylation and that Src also prevents PTEN translocation to plasmamembrane by directly phosphorylating PTEN on tyrosine residues. Indeed,PEPD (2.7 nM, 0.5 h) inhibited PTEN tyrosine phosphorylation in bothCHO-K1/ErbB2 cells and BT-474 cells (FIG. 5f ), and PTEN translocationfrom cytoplasm to plasma membrane increased after PEPD treatment (2.7nM, 1 h) (FIG. 5g ).

Example 6

This Example demonstrates that PEPD targets cells overexpressing ErbB2.Our finding of PEPD binding to ErbB2 and the ensuing changes issummarized in FIG. 6a . The rapid inhibition of Src which plays a majorrole in ErbB2 oncogenesis along with strong ErbB2 depletion suggestedthat PEPD might inhibit cells overexpressing ErbB2. The potentialinhibitory effects of PEPD on CHO-K1 cells, CHO-K1/ErbB2 cells andBT-474 cells were evaluated using three assays as described below.

The effect of PEPD on DNA synthesis was measured by BrdU incorporationvia flow cytometry. Cells were treated by PEPD at 2.7 and 27 nM for 48h. While PEPD was ineffective in CHO-K1 cells, it reduced the number ofBrdU-positive CHO-K1/ErbB2 cells and BT-474 cells by up to 65% and 50%,respectively (FIG. 6b ). To measure the effect of PEPD onanchorage-independent growth, cells were grown in soft agar and treatedwith PEPD at 2.7 and 27 nM for 21 days with medium change of every 3-4days. Colony formation was not significantly affected by PEPD in CHO-K1cells but was markedly inhibited by PEPD in both CHO-K1/ErbB2 cells andBT-474 cells. PEPD reduced the number of colonies with diameter of ≥100μm in CHO-K1/ErbB2 cells and BT-474 cells by up to 50% and 57%,respectively (FIG. 6c ). The effect of PEPD on cell invasion andmigration was measured using BD BioCoat Matrigel Invasion Chambers.Cells were grown in the upper chamber and treated with solvent or PEPDat 2.7 and 27 nM for 48 h, and the cells that invaded through theMatrigel membrane at the bottom of the upper chamber were counted. PEPDwas ineffective in CHO-K1 but inhibited the invasion and migration ofCHO-K1/ErbB2 cells and BT-474 cells by up to 50% and 51%, respectively(FIG. 6d ). Collectively, these results confirm that the impact of PEPDon ErbB2 is predominantly inhibitory and also show that PEPD selectivelytargets cells overexpressing ErbB2.

It will be apparent from the foregoing data that the present disclosurebreaks the long spell of ErbB2 being believed to be an orphan receptor.Compared to other ligands of ErbB receptors, several unusualcharacteristics of human PEPD are notable: it does not have an EGFmotif; it apparently binds to ErbB2 as a homodimer; and it suppressesthe oncogenic signaling of ErbB2. PEPD binds to both ErbB2 monomer andErbB2 dimer, but as shown in FIG. 1f , PEPD binds to ErbB2 homodimersmore rapidly than to ErbB2 monomers. This explains why PEPD causes varyrapid disruption of ErbB2-Src signaling (FIG. 5) but somewhat slow ErbB2phosphorylation (FIG. 2a ).

When evaluated for its effect on cell growth and proliferation, PEPD wasineffective in CHO-K1 cells that expressed a low level of ErbB2 butshowed strong inhibitory activities in ErbB2-overexpressing CHO-K1 cells(CHO-K1/ErbB2 cells) and BT-474 cells, including inhibition of DNAsynthesis, anchorage-independent growth, and invasion and migration(FIGS. 6b-6d ). This shows that PEPD targets ErbB2 oncogene addiction,as CHO-K1/ErbB2 cells were derived from CHO-K1 cells; at least twomechanisms may be involved: PEPD causes ErbB2 depletion by inducingErbB2 internalization and degradation, and PEPD inhibits ErbB2-Srcsignaling by disrupting their association (FIG. 5). The effects of PEPDon ErbB2 resemble that of trastuzumab, an ErbB2-targeting monoclonalantibody which binds to subdomain 4 of ErbB2 ECD and is used currentlyfor treating ErbB2-positive breast cancers. Data presented in theforegoing examples show that at equimolar concentrations, inhibition ofproliferation of CHO-K1/ErbB2 cells and BT-474 cells by PEPD or itsG278D mutant was similar to, if not better than that by trastuzumab,while none of the agents showed inhibitory activity in CHO-K1 cells(FIG. 14). Recombinant human PEPD or its mutant, produced in bacteria,may potentially be a low cost alternative to the highly expensivetrastuzumab which must be produced in mammalian cells. Moreover, asmentioned before, in vivo, trastuzumab neither down regulates ErbB2expression nor inhibits ErbB2 tyrosine phosphorylation in cancertissues; rather, its antitumor activity depends mainly onantibody-dependent cell-mediated cytoxicity (ADCC) via its Fc domain.Thus, PEPD or its mutant may synergizes with trastuzumab or overcome tocertain extent the resistance to trastuzumab in patients. PEPD does notbind to ErbB3 and ErbB4 (FIG. 1a ), but it is well known that ErbB2 is apreferred heterodimerization partner with these ErbBs. This raises thequestion of whether blockade of ErbB2 oncogenic signaling by PEPD mayalso include inhibition of ErbB2 heterodimer signaling units. Notably,in human breast cancer, the oncogenic activity of ErbB2 dependscritically on ErbB3. It will be apparent to those skilled in the artthat the present disclosure reveals a fundamentally new function ofhuman PEPD: an ErbB2 ligand independent of its dipeptidase activity.PEPDs from many species share high sequence homology with human PEPD andmay also bind and modulate ErbB2.

In view of in vitro results described in Examples 1-6, which stronglysupport the use of PEPD as an agent for treating Erb2 positive cancers,we tested PEPD and the enzymatically inactive version of it in vivo todetermine its efficacy against ErbB2 positive cancers in clinicallyrelevant animal models, as described in the following Examples.

Example 7

This Example demonstrates using recombinant human PEPD and its mutantPEPD^(G278D) in vivo as an anticancer agent. As was the case in the invitro experiments shown in Examples 1-6, the data presented in thisexample were obtained using recombinant human PEPD and its mutantPEPD^(G278D) with 6×His tagged to the carboxy terminus that weregenerated in E. coli and purified by affinity chromatography using a HIStag engineered into these proteins. These products were used in thefollowing experiments.

First, we carried out dose-finding experiments. In vitro, PEPD atconcentrations as low as 2.7 nM was effective againstErbB2-overexpressing cells. Adult C57BL/6 mice were given a singleintraperitoneal dose of PEPD, and mice were killed for blood collectionat 1, 6 or 24 h post dosing. While giving PEPD at 10 mg/kg elevatedplasma PEPD to 16.5 nM at 1 h and 13.6 nM at 24 h post dosing, comparedto 0.9 nM in the control mice, giving PEPD at 0.2 mg/kg unexpectedlyresulted in 51-61% decrease in plasma PEPD level (FIG. 14a ). However,we discovered that combining the PEPD agents with enoxaparin (EP), whichis a clinically used small molecular weight heparin and is known toinhibit factor Xa and other coagulation factors, results in persistenceof PEPD, as plasma level of PEPD following PEPD dosing at 0.2 mg/kg wereup to 64 fold higher in EP-pretreated mice than in mice without EPtreatment (FIG. 14b ). Without intending to be constrained by anyparticular theory, it is believed that the EP may be reducingdegradation of the PEPD. It is plausible that other coagulationinhibitors will also be effective in maintaining PEPD plasmaconcentration in vivo. Next, we analyzed whether PEPD inhibits thegrowth of ErbB2-overexpressing tumors in vivo. CHO-K1/ErbB2 cells, whichstably overexpress human ErbB2 but do express any other ErbB familyreceptors, were inoculated subcutaneously to the flanks of femaleathymic nude mice (6-7 weeks of age) at 1×10⁶ cells per site in a smallvolume of PBS:Matrigel mix. Starting 4 days after cell inoculation, themice were given either vehicle or EP at 2.5 mg/kg by intraperitonealinjection once daily. Three days after EP treatment was started (on day7 after cell inoculation), when tumor volume reached approximately 41mm³, the EP-treated mice were also treated with vehicle or PEPD at 0.02mg/kg or 0.2 mg/kg by intraperitoneal injection, which was given threetimes per week (Monday, Wednesday, Friday). Notably, on the days whenboth EP and vehicle/PEPD were given, vehicle or PEPD was always given 1h after EP dosing. Tumor volume was measured three times per week(Monday, Wednesday, Friday) by length×width²/2. The mice were killed 24h after the last treatment which was given on day 24 after cellinoculation (a total of 8 PEPD treatments), and blood samples werecollected from the mice for measurement of plasma levels of PEPD byELISA. While EP had no effect on tumor growth, EP plus PEPD at 0.02 and0.2 mg/kg inhibited tumor growth by 27% (statistically insignificant)and 65% (highly statistically significant), respectively (FIG. 15a ).Plasma levels of total PEPD (endogenous mouse PEPD plus human PEPD) atthe end of the experiment were 1.9 nM in EP only group, 5.5 nM in EPplus low dose PEPD group, and 33.0 nM in EP plus high dose PEPD group,which are 1.4-, 4.2-, 24.8-fold higher than in the control mice (FIG.15b ).

We next analyzed whether PEPD specifically targets ErbB2-overexpressingtumors in vivo. CHO-K1 cells which express negligible ErbB2 and do notexpress other ErbBs were inoculated subcutaneously to the flanks offemale athymic nude mice (6-7 weeks of age) at 1×10⁶ cells per site in asmall volume of PBS; Matrigel mix. Starting 4 days after cellinoculation, the mice were treated with EP at 2.5 mg/kg byintraperitoneal injection once daily. Three days later (on day 7 aftercell inoculation), when the tumor volume reached approximately 26 mm³,the mice were also treated with vehicle or PEPD at 0.2 mg/kg byintraperitoneal injection, which was given three times per week (Monday,Wednesday, Friday). On the days when both EP and PEPD/vehicle weregiven, PEPD/vehicle was always given 1 h after EP administration. Tumorvolume was measured three times per week (Monday, Wednesday, Friday).The mice were killed 24 h after the last treatment which was given onday 21 after cell inoculation (a total of 7 PEPD treatments), and bloodsamples were collected from the mice for measurement of plasma level ofPEPD. PEPD treatment had no effect on tumor growth (FIG. 16a ), eventhough plasma levels were elevated as expected (FIG. 16b ). Thus, ourdata presented herein demonstrates that PEPD specifically targets tumorscomprising cells which overexpress ErbB2.

Next, the effect of PEPD was evaluated in an orthotopic breast tumormodel. Human breast cancer BT-474 cells constitutively overexpress ErbB2and have been widely used to generate orthotopic breast tumors forevaluation of anti-ErbB2 therapies. Female athymic nude mice (6-7 weeksof age) were each implanted subcutaneously with a 60-day release of17β-estradiol pellet (1.7 mg of estradiol, purchased from InnovativeResearch of American) prior to orthotopic inoculation of BT-474 cellsinto the mammary fat pads (2×10⁶ cells per site in a small volume ofPBS:Matrigel mix). Twenty three days after cancer cell inoculation, allmice began daily treatment of EP at 0.5 mg/kg daily by intraperitonealinjection. Notably, a dose-finding experiment showed EP at 0.5 mg/kg wasas effective as 2.5 mg/kg in maintaining PEPD concentration in theblood. Also, another group of mice that were implanted with17β-estradiol and then inoculated with BT-474 cells were kept as ano-treatment control, in order to confirm that EP itself did not haveany effect on tumor growth. The no-treatment mice were kept for 58 daysafter cancer cell inoculation (FIG. 17a ). The EP-treated mice wererandomized to three groups to receive vehicle, PEPD, and PEPD^(G278D),while daily EP treatment continued Based on our experience with PEPD inthe CHO-K1/ErbB2 tumor model, we decided to treat mice with PEPD or itsmutant at 2 mg/kg. Treatment with vehicle, PEPD or its mutant wasstarted 4 days after the start of EP treatment (on day 27 after cancercell inoculation), and each was given by intraperitoneal injection threetimes per week (Monday, Wednesday, Friday). When EP was also given onthe same day, it was always given 1 h earlier than the other agent.Tumor volume was measured on Monday, Wednesday and Friday every week. Asshown in FIG. 17a , EP had no effect on tumor growth, but both PEPD andPEPD^(G278D) rapidly caused tumor shrinkage. PEPD^(G278D) was moreeffective than PEPD (the difference in tumor volume between the twogroups is statistically significant). In view of the strong antitumorefficacy of the agents, all treatments were stopped 1 month later (lastdose was given on day 58 after cancer cell inoculation), and the micewere kept for observation. A small volume of blood was also obtainedfrom the mice 24 h after the last dose for measurement of plasma PEPDlevel. Plasma PEPD level in mice treated with EP only was 1.9 nM,1.4-fold higher than in mice with no treatment (FIG. 17b ), againshowing that EP significantly facilitates persistence of endogenousmouse PEPD. Moreover, plasma PEPD levels in the mice treated with EPplus PEPD and EP plus PEPD^(G278D) were 154.3 nM and 128.6 nM,respectively, which are 111.0- and 92.5-fold higher than in mice with notreatment (FIG. 10b ). A second 17β-estradiol pellet was implanted toeach mouse on day 59 after cancer cell inoculation. Three weeks aftertreatment stop (on day 80 after cancer inoculation), tumors in some micethat were previously treated with PEPD or its mutant regrew. However,50% of the mice treated with PEPD^(G278D) remained tumor-free and 27% ofthe mice treated with PEPD remained tumor-free (FIG. 17a ), anotherindication that PEPD^(G278D) is more effective than PEPD. All mice withtumor regrowth were retreated with EP plus PEPD^(G278D): Daily EP at 0.5mg/kg by intraperitoneal injection was started on day 89 after cancercell inoculation, and PEPD^(G278D) was administered at 2 mg/kg byintraperitoneal injection every other day for a total of 4 doses. Asdescribed before, on days when both EP and PEPD^(G278D) were given, EPwas given 1 h earlier. The experiment was terminated 24 h after the lastPEPD^(G278D) dose. As shown in FIG. 17a , all tumors were stillexquisitely sensitive to PEPD^(G278D), indicating that tumor regrowthwas not due to the presence of cancer cells that were resistant to PEPDor PEPD^(G278D), but rather it was due to incomplete initial eradicationof cancer cells. In addition, the mice previously treated with EP onlywere re-treated with EP at 0.5 mg/kg once daily, which was started onday 82 after cancer cell inoculation, and 4 days later, the mice weredivided into two groups: vehicle treatment or treatment withPEPD^(G278D) at 2 mg/kg, which were given three times per week (Monday,Wednesday, Friday) by intraperitoneal injection for a total of 5 doses.The experiment was terminated 24 h after the last dose. As shown in FIG.17a , PEPD^(G278D) caused rapid shrinkage of tumor volume, even thoughthe tumors were extremely large at the beginning of the treatment. It isalso important to note that the significant antitumor efficacy of PEPDand PEPD^(G278D) was not associated with any toxicity: no effect onmouse body weight gain or the weight of the organs such as colon, heart,kidney, liver, lung and stomach. This indicates that the agents at thetherapeutically effective doses are not toxic.

Example 8

This Example provides a demonstration of making a PEPD-Fc hybrid(fusion) protein.

Trastuzumab, which binds to subdomain 4 in ErbB2 extracellular domain,is the most successful and most widely used anti-ErbB2 agent in breastcancer. However, the overall response rate to trastuzumab remainsmodest, and primary and secondary resistance remains a clinicalchallenge. The Fc domain of trastuzumab is critical for its antitumoractivity by engaging Fc receptors on immune effector cells and elicitingantibody-dependent cell-mediated cytotoxicity. In fact, a clinical studyfound that trastuzumab at dose levels used for treating ErbB2-positivebreast cancers had no ability to down regulate ErbB2 proteins in thecancer tissues (Gennari R, et al. Clinical Cancer Research 2004, 10(17):5650-5655). Fc is also known to promote blood persistence of antibodies.However, PEPD does not have a Fc domain.

We conducted tests aiming at making and determining whether adding Fc toPEPD boost its antitumor activity would be plausible. The PEPD-Fc hybridmolecule may also be retained in the blood to a higher level and for alonger time than PEPD is. We have generated PEPD-Fc (monomer molecularweight: 80.9 kD). Briefly, the full coding sequence of human PEPD wassubcloned to the pFUSE-hIgG1-Fc vector (InvivoGen), linked in frame atits C terminus to the Fc sequence of human IgG1. The resultant construct(pFUSE-PEPD-Fc) was verified by sequencing and transfected to CHO-K1cell, and the expressed hybrid protein in the cell lysates was purifiedusing Protein A-Sepharose. High purity of PEPD-Fc was confirmed bySDS-PAGE. The bioactivity of PEPD-Fc was compared to that of PEPD.CHO-K1/ErbB2 cells were treated with vehicle, PEPD-Fc or PEPD (both at27 nM) for 3 h or 6 h. PEPD-Fc caused time-dependent and significantErbB2 protein depletion, but was somewhat less effective than PEPD (FIG.18). It is possible that PEPD-Fc may simply be slightly slower than PEPDin causing ErbB2 depletion, and increasing treatment time may allowPEPD-Fc to achieve the same impact on ErbB2 as PEPD does. Nevertheless,as shown in FIG. 18, the two agents showed very similar impact on ErbB2phosphorylation and ERK phosphorylation, and on silencing ErbB2-Srcsignaling (decreasing phosphorylation of Src, PTEN and AKT). Our resultsindicate that PEPD-Fc largely if not totally retains theErbB2-modulating activity of PEPD. Given that PEPD-Fc is expected toengage immune cells in vivo, it may be significantly more powerful thanPEPD or PEPD^(G278D) in combating ErbB2-positive cancers.

Given the benefit of the present disclosure, PEPD-Fc hybrid andPEPD^(G278D)-Fc can be readily evaluated in animal models. Inembodiments, these hybrids will be generated in mammalian cells (e.g.,CHO-K1 cells) to ensure glycosylation at N297 of Fc, which is essentialfor Fc function. Interestingly, aglycosylated Fc with certain mutationsmaintains its bioactivity, including but not limited to Fc^(T299A) andFc^(E382V/M428I). Thus, additional hybrids with specific mutations tothe Fc sequence can be generated, such as in E. coli and evaluated usingconventional techniques, given the benefit of the present invention.

Example 9

As can be seen from FIG. 17a , and FIGS. 19(a)-(e) which summarize dataobtained by measuring in vivo changes in tumors treated by rhPEPD orrhPEPD^(G278D), rhPEPD^(G278D) is superior to rhPEPD with respect toreducing tumor volume in vivo (FIG. 17a and FIG. 19(a)). Withoutintending to be bound by any particular theory, we believe this isrelated to the novel discovery that rhPEPD^(G278D) does not stimulateHIF-1α signaling, whereas PEPD does (FIG. 19(e)). In this regard, it iswell known in the art that VEGF and GLUT-1 are downstream targets ofHIF-1α, and the differing effects on these markers are similar to theeffect on HIF-1α. All three are well-known prosurvival factors. However,we also observed that both PEPD and PEPD^(G278D) obliterated ErbB2signaling, inactivating ErbB3, as well as activating apoptosis in thetumor tissues. Both agents caused ErbB-2 depletion, ErbB2dephosphorylation (inactivation), dephosphorylation (inactivation) ofSRC, AKT, ERK, ErbB3, down regulation of anti-apoptotic Bcl-2,proapoptotic BAX, and activation of multiple caspases in the tumortissues (FIG. 19b ). Both agents also reduced SRC kinase activity andPI3K activity in the tumor tissues (FIG. 19c ). We also found both PEPDand PEPD^(G278D) were internalized by tumor cells to similar extent, asmeasured by their His tag (FIG. 19e ). This finding supports the conceptthat PEPD or PEPD^(G278D) may be conjugated to a toxin or a cancerchemotherapeutic agent, as discussed before, for enhanced anticancerefficacy.

It is notable that in vivo, trastuzumab/herceptin neither down regulatesErbB2 expression nor inhibits ErbB2 tyrosine phosphorylation in cancertissues (Gennari et al., Clinical Cancer Research, 10, 5650-5655, 2004;Gijsen et al., PLoS Biology, 8, e1000563, 2010). Rather, herceptinrelies mainly on antibody-dependent cell-mediated cytoxicity (ADCC).Thus, based on the data presented herein, it is plausible thatrhPEPD^(G278D) may complement herceptin or overcome certain herceptinresistance.

Example 10

This Example provides a description of the materials and methods thatwere used to obtain the data described in Examples 1-9.

Reagents.

Recombinant chimeras, including human ErbB2/ECD-Fc (1129-ER-050), humanErbB3/ECD-Fc (348-RB-050) and human ErbB4/ECD-Fc (1131-ER-050) as wellas recombinant Fc of human IgG₁ (110-HG-100) were from R&D systems.Recombinant human EGF (236-EG-200) and human NRG-1 (5218) were purchasedfrom R&D Systems and Cell Signaling, respectively. Trastuzumab(Genentech) was obtained from Roswell Park Cancer Institute Pharmacy.4-Aminophenylmercuric acid (APMA), crystal violet,methylthiazolyldiphenyl-tetrazolium bromide (MTT) and vanadate were fromSigma-Aldrich. The following antibodies were used: anti-PEPD (Abcam,ab86507), anti-PTEN (Santa Cruz, sc-7974), anti-p-PTEN (Santa Cruz,sc-101789), anti-p-Tyr (PY99) (Santa Cruz, sc-7020), anti-CK2a (SantaCruz, sc-12738), anti-ECD of ErbB2 (Santa Cruz, sc-134481), anti-ErbB3(Santa Cruz, sc-285), anti-TGFα (Santa Cruz, sc-9043), anti-ErbB2 (CellSignaling, 2165), anti-p-ErbB2 (Y1196) (Cell Signaling, 6942),anti-p-ErbB2 (Y1221/1222) (Cell Signaling, 2243), anti-ErbB1 (CellSignaling, 2232), anti-ErbB4 (Cell Signaling, 4795), anti-PI3K p85 (CellSignaling, 4257), anti-p-Src (Cell Signaling, 6943), anti-Src (CellSignaling, 2123), anti-AKT (Cell Signaling, 4691), anti-p-AKT (CellSignaling, 4060), anti-ERK (Cell Signaling, 9102), anti-p-ERK (CellSignaling, 9101), anti-ubiquitin (Santa Cruz, sc-8017), anti-GAPDH(Millipore, MAB374), anti-human IgG₁ for detection of Fc (Santa Cruz,sc-2453), FITC-conjugated anti-His-tag (Abcam, ab1206),biotin-conjugated anti-His-tag (Bethyl, A190-113B), and TRITC-conjugatedgoat-anti-rabbit (Jackson, 111-025-003). HRP-conjugated streptavidin(N100) was from Thermo Scientific.

Recombinant human PEPD and its mutants (6×His tagged to the carboxyterminus) were generated in bacteria and purified using nickel affinitychromatography (Qiagen). The purity of each protein was confirmed by gelelectrophoresis and silver staining (FIG. 10b ). Details for thepreparation of PEPD and its mutants as well as other reagents areprovided below.

The bacterial pBAD/TOPO ThioFusion expression system (Invitrogen) wasused to produce and purify PEPD and the PEPD mutants. In brief,pCMV6-XL5-PEPD (Origene) was used as a template to amplify the fulllength human PEPD by PCR using primers For-5′-AATACGACTCACTATAGGGCG-3′(SEQ ID NO:2) and Rev-5′-CTTGGGGCCAGAGAAGG-3′ (SEQ ID NO:3), which weredesigned to express PEPD as a native protein with 6×His tagged to thecarboxy terminus (but without the N-terminal Thio). The resulting PCRfragments were subcloned into the pBAD/Thio-TOPO expression vector by TAcloning. The construct was sequenced to ensure the integrity of theentire coding sequence. Expression and purification were performed asindicated by the manufacturer. The PEPD G278D mutant as well as othermutants, which include the N-terminal 184 amino acids fragment, theN-terminal 265 amino acids fragment, and the C-terminal 265 amino acidsfragment, were generated by site-directed mutagenesis using theQuikChange Lightning Multi Site-Directed Mutagenesis kit (AgilentTechnologies) and using the above-described PEPD expression vector asthe template. The constructs were sequenced to ensure the correctmutation. Both the wild-type PEPD and mutant PEPD were purified viaNi-NTA Agarose Chromatography (Qiagen). The proteins were furtherpurified using Ultracel YM-30 Centricon (Millipore). SDS-PAGE wasperformed in 8-10% acrylamide gels under denaturing and reducingconditions, and the gels were stained with Silver staining to examineprotein purity. The preparations were also checked for potentialcontamination of lipopolysaccharides, using the E-TOXATE Kit (Sigma),following the manufacturer's instruction, but no lipopolysaccharideswere detected (detection limit: 0.005 endotoxin unit per 0.1 ml sample).

Cell Lines and Cell Culture.

BT-474 cells and CHO-K1 cells were from ATCC. CHO-K1/ErbB2 cells weregenerated by transfecting CHO-K1 cells with pcDNA3-ERBB2 and selectedunder G418. CHO-K1 cells and CHO-K1/ErbB2 cells were cultured in F-12Kmedium (Gibco) supplemented with 10% FBS (Gibco). BT-474 cells werecultured in 50% high-glucose DMEM (Mediatech)/50% F-12K mediumsupplemented with 10% FBS. Human breast cancer MCF-7 cells and humanbladder cancer RT-4 cells, from ATCC, were also used in the study. MCF-7cells and RT-4 cells were cultured in high-glucose DMEM plus 10% FBS andMcCoy′SA medium plus 10% FBS, respectively. All cells were cultured inhumidified incubators at 37° C. with 5% CO₂.

Gene Transfection and Plasmids.

Cells were grown in 6-well plates and transfected with a plasmid usingFuGENE HD (Promega) or Lipofectamine 2000 (Invitrogen). pCMV6-XL5-PEPDexpressing wild-type human PEPD was from Origene. pMT107-His-Ub was usedto express ubiquitin. pCMV6-XL5-ERBB2 expressing human ErbB2 wasgenerated by cloning full length human ERBB2 coding sequence to themammalian expression vector pCMV6-XL5 (Origene). To constructpCMV6-XL5-ERBB2 which expresses human ErbB2, the full length human ERBB2coding sequence was amplified by PCR from the LNCaP cDNA usingNotI-forward primer (5′-ATAAGAATGCGGCCGCAGCTGAGATTCCCCTCCATT-3′) (SEQ IDNO:4) and NotI-reverse primer(5′-ATAGTTTAGCGGCCGCCTTGATGCCAGCAGAAGTCA-3′) (SEQ ID NO:5). AmplifiedPCR products were digested by NotI (New England BioLabs), followed byligation into pCMV6-XL5 (Origene) which was pre-digested with the samerestriction enzyme. The orientation of the insert was determined bycolony PCR using forward primer 5′-CAAATGGGCGGTAGGCGTGTA-3′ (SEQ IDNO:6) (localized to the plasmid) and reverse primer5′-ATTGGTGGGCAGGTAGGTGAGTTC-3′ (SEQ ID NO:7) (annealed to the beginningof the insert). The construct was sequenced to confirm the integrity ofthe entire coding sequence. All site-directed mutations and deletions inthe ERBB2 gene were performed on pCMV6-XL5-ERBB2, using the QuikChangeLightning Site-Directed Mutagenesis Kit. These constructs include ErbB2that carries K753M mutation (pCMV6-XL5-ERBB2/K753M), deletion of ErbB2ECD subdomain 1 (pCMV6-XL5-ERBB2/delD1, deletion of amino acids 1-195),deletion of ErbB2 ECD subdomain 2 (pCMV6-XL5-ERBB2/delD2, deletion ofamino acids 196-320), deletion of ErbB2 ECD subdomain 3(pCMV6-XL5-ERBB2/delD3, deletion of amino acids 321-488), and deletionof ErbB2 ECD subdomain 4 (pCMV6-XL5-ERBB2/delD4, deletion of amino acids489-560). All constructs were sequenced to ensure the correctmutation/deletion.

Western Blot Analysis.

Preparation of cell lysates, measurement of protein concentration andwestern blot were performed using standard techniques. Cell membrane,cytosol fractions or cell lysates minus cell membrane were preparedusing the Mem-PER Eukaryotic Membrane Protein Extraction Reagent Kit(Thermo Scientific). Cell culture medium was concentrated 20 fold usingCentricon (Millipore) before analysis. In experiments measuring thebinding of PEPD or NRG-1 to ErbB2 ECD, ErbB3 ECD or ErbB4 ECD, a silverstaining kit (Invitrogen) was used to display the proteins after gelelectrophoresis. To detect ErbB2 receptor dimerization, PEPD-treatedcells and control cells were washed with ice-cold PBS and incubated withcross linker BS3 (Pierce) at 2 mM for 30 min at room temperature. Thecross-linking reaction was terminated by adding 50 mM Tris (final,pH7.5), followed by incubation at room temperature for 15 min. Celllysates were analyzed by western blotting (3.5% SDS-PAGE). Non-reducinggel electrophoresis was used to determine, besides the wild type humanPEPD, whether any of its mutants, including G278D-PEPD, R184X-PEPD,R265X-PEPD, and X265R-PEPD, existed as a homodimer. Briefly, eachprotein sample was mixed with non-reducing sample buffer (sample loadingbuffer without β-mercaptoethanol) and then resolved by 10% SDS-PAGE,before silver staining. Protein concentrations of all specimens weremeasured by the Bicinchoninic Acid Assay (BCA) Kit (Pierce).

Immunoprecipitation.

PEPD was incubated with ErbB2/ECD-Fc, ErbB3/ECD-Fc, ErbB4/ECD-Fc or Fcin binding buffer for 2 h at 37° C., followed by pull down with proteinG-sepharose beads. The immunoprecipitates were washed with IP washingbuffer and analyzed by western blotting. For detection of direct andspecific binding of PEPD or NRG-1 to ErbB2, ErbB3 or ErbB4, recombinanthuman PEPD or NRG-1 was incubated with recombinant human ErbB2/ECD-Fc,recombinant human ErbB3/ECD-Fc, recombinant human ErbB4/ECD-Fc orrecombinant human Fc in 0.4 ml binding buffer. All solutions wereincubated for 2 h at 37° C., followed by incubation with proteinG-sepharose beads for 1 h at room temperature. The immunoprecipitateswere washed with IP washing buffer and then subjected to western blotanalysis. In experiments using whole cell lysates, cells were lysed inM-PER buffer supplemented with a proteinase inhibitor mix (Roche AppliedScience), and the lysates were incubated with a specific antibodyovernight at 4° C., followed by pull down by protein G-agarose. Theimmunoprecipitates were washed with IP washing buffer and analyzed bywestern blotting. To measure the effect of PEPD on PTEN tyrosinephosphorylation, cells were pretreated with 30 μM pervanadate for 10 minto inhibit relevant tyrosine phosphatase and then treated with PEPD orvehicle, followed by preparation of cell lysates for analysis.Pervanadate was prepared fresh by incubating 10 mM vanadate with 10 mMhydrogen peroxide for 15 min at room temperature, followed by additionof catalase (Sigma) at final concentration of 0.2 mg/ml to removeresidual hydrogen peroxide.

ELISA-Based Measurement of PEPD and PEPD Binding to ErbB2.

To measure PEPD binding to human ErbB2 or its deletion mutants, ELISAplates were coated overnight at 4° C. with 100 μl/well of an ErbB2antibody (binding to the cytoplasmic tail of ErbB2) at 10 μg/ml. Afterwashing the wells three times with PBST, residual protein binding sitesin the wells were blocked by incubation for 2 h at room temperature with300 μl/well of 1% BSA in PBS. Following addition of 60 μl of seriallydiluted recombinant human PEPD into each well, 60 μl of cell lysates(prepared from CHO-K1 cells transfected with the empty vector for 24 hand CHO-K1 cells transfected with wild-type ErbB2 for 24 h), containing25 μg of total protein per sample (note: a preliminary experiment usingup to 250 μg of total protein per sample showed similar outcome of PEPDbinding to ErbB2), were added to each well and incubated at 37° C. for 2h. After three washes with PBST, 100 μl of a biotin-conjugated anti-Hisantibody (1:10,000 dilution; note that PEPD is His-tagged) was added toeach well and incubated for 2 h at room temperature. After another roundof washing with PBST, 100 μl of streptavidin-conjugated HRP (1:10,000dilution) was added to each well and incubated for 45 min at roomtemperature. After another round of washing with PBST, 100 μl/well of 1×substrate solution (3,3′,5,5′-tetramethylbenzedine) was added, and afteradequate color development, 100 μl/well of stop solution (1 N H₂SO₄) wasadded and absorbance reading at 450 nm was recorded. In experimentscomparing PEPD binding to wild-type ErbB2 and its deletion mutants(deletion of subdomains 1, 2, 3 or 4 in the ErbB2 ECD), an equal amountsof wild-type ErbB2 protein and its mutants were used. The lysates ofcells transfected with the plasmid expressing each protein (for 24 h)were first subjected to western blot analysis, followed by densitometrymeasurement of the specific protein bands normalized to a loadingcontrol, to calculate the amount of lysates that deliver the same amountof each protein (25 μg of total protein/sample were used for lysatescarrying the wild-type ErbB2).

Measurement of PEPD Concentration by ELISA.

To measure PEPD concentrations, 96-well ELISA plates were coated with100 μl/well of diluted anti-PEPD mouse monoclonal antibody (2.5 μg/ml)at 4° C. overnight. The plates were then washed three times withphosphate buffered saline with Tween 20 (PBST) and blocked with 200μl/well of blocking buffer (incubation for at least 2 h at roomtemperature). The plates were washed with PBST and then incubated with100 μl/well of PEPD standard or samples, which were appropriatelydiluted, for 2 h at room temperature. The plates were washed three timeswith PBST, and each well was then incubated with 100 μl of a detectionantibody (an anti-PEPD rabbit polyclonal antibody) for 2 h at roomtemperature. After washing the plates three times with PBST, 100 μl ofsecondary reagent (goat-anti-rabbit IgG-HRP) were added to each well,followed by 1 h incubation at room temperature. The plates were washedagain with PBST three times, and each well was then incubated with 100μl of a HRP substrate solution (3,3′,5,5′-tetramethylbenzedine substratefrom Cell Signaling, #7004). After adequate color development, 100 μl ofstop solution (Cell Signaling, #7002) was added to each well, andabsorbance at 450 nm was recorded by a microtiter plate reader. PurePEPD was used as a standard.

Immunofluorescence Staining and Confocal Microscopy.

Cells were grown in chamber slides (1.5×10⁴ cells/well) overnight,followed by treatment with PEPD or vehicle. The cells were then washedwith ice-cold PBS, fixed with 4% paraformaldehyde for 15 min at roomtemperature, washed again with ice-cold PBS, and blocked with 1% BSA inPBS for 45 min at room temperature. The cells were then incubated withan ErbB2 antibody for 1 h at room temperature, washed with PBS,incubated with a FITC-conjugated His-tag antibody (for PEPD detection)and a TRITC-conjugated secondary antibody (for ErbB2 detection) for 1 hat room temperature, and washed again with PBS. The cells were thenexamined with a Zeiss LSM 510 confocal microscope.

RT-PCR.

Total RNA was isolated using the RNeasy Mini Kit (Qiagen), and aftertreatment with TURBO DNase to remove potential genomic DNAcontamination, 500 ng RNA per sample was reverse transcribed into cDNAin 25 μl reaction using the TaqMan Reverse Transcription Reagents(Invitrogen). The RT reaction was performed at 25° C. for 10 min,followed by heating at 48° C. for 30 min, and then 95° C. for 5 min.Each PCR amplification was carried out in 20 μl volume, containing 10 μlGoTaq Master Mix (2×) (Promega), 0.5-1 μl of the reverse-transcribedmixture (cDNA), 0.25 μM each of specific forward and reverse primers.The primers are as follows: human ERBB2, forward,5′-CTGTTTGCCGTGCCACCCTGAGT-3′ (SEQ ID NO:8), reverse,5′-CTTCTGCTGCCGTCGCTTGATGAG-3′ (SEQ ID NO:9); human GAPDH, forward,5′-CCAGGGCTGCTTTTAACTC-3′ (SEQ ID NO:10), reverse,5′-GCTCCCCCCTGCAAATGA-3′ (SEQ ID NO:11); Chinese hamster GAPDH, forward,5′-TGGAATCTACTGGCGTCTTC-3′ (SEQ ID NO:12), reverse,5′-CACCACCTTCTTGATGTCCT-3′ (SEQ ID NO:13). The PCR conditions used forall reactions are as follows: 94° C. for 3 min, 28 cycles (humanERBB2)/25 cycles (GAPDH) at 94° C. (denaturation) for 30 sec, 63° C.(human ERBB2)/60° C. (human GAPDH)/56° C. (Chinese hamster GAPDH) for 30sec (annealing), and 72° C. for 30 sec (extension); the final extensionwas performed at 72° C. for 5 min. The PCR products were analyzed byelectrophoresis with 1% agarose gel, stained by ethidium bromide, andvisualized under UV light.

BrdU Assay.

BrdU incorporation into DNA was measured using the FITC BrdU Flow Kit(BD Pharmingen). Briefly, cells were grown in 6-well plates (0.15×10⁶cells/well for CHO-K1 cells and CHO-K1/ErbB2 cells, 0.4×10⁶ cells/wellfor BT-474 cells; 2 ml medium/well) overnight, treated with vehicle orPEPD for 48 h, and then incubated with BrdU at 10 μM in culture mediumfor 30 min (CHO-K1 cells and CHO-K1/ErbB2 cells) or 18 h (BT-474 cells).The cells were then harvested, fixed and permeabilized infixation/permeabilization buffer, treated with NDase for 1 h at 37° C.,and incubated with a BrdU antibody for 20 min at room temperature,followed by DNA staining with 7-amino-actinomycin D. The stained cellswere resuspended in 0.5-1 ml of staining buffer per sample and analyzedby a flow cytometer (BD FACS Calibur, BD Biosciences), counting 10,000cells per sample. BrdU incorporation was modeled using the WinMDI 2.8software.

Soft Agar Colony Formation Assay.

After 1 ml of 0.8% ultrapure Noble Agar (USB, cat#10907) in culturemedium was solidified in each well of 6-well plates, 1 ml of cells(2×10⁴ BT-474 cells, 1×10³ CHO-K1 cells or 1×10³ CHO-K1/ErbB2 cells)suspended in 0.4% agar in culture medium at 37° C. were added to eachwell, which also solidified afterwards. PEPD or vehicle was then addedin 2 ml of medium to each well, which was changed every 3-4 days for atotal of 21 days. At the end of this treatment, cell colonies of ≥100 μmin diameter were counted under a dissection microscope (Axiovert 40 CFL,Carl Zeiss) in 10 different fields (10× magnification) per well, aidedby ImageJ.

Cell Invasion and Migration Assay.

Cell invasion and migration were measured using the BD BioCoat MatrigelInvasion Chambers (BD Biosciences). Briefly, the lower chamber wasfilled with 0.75 ml medium with 10% FBS, and the upper chamber wasplaced with 4×10⁴ cells suspended in 0.5 ml of serum-free mediumcontaining vehicle or PEPD. The chambers were placed in a cell cultureincubator at 37° C. for 48 h. At the end of the incubation, the cellsthat invaded through a Matrigel matrix layer coated on the filter insertwhich was placed at the bottom of the invasion chamber were fixed with100% methanol, stained with 0.5% crystal violet, and counted under amicroscope (Eclipse 50i) in 10 different fields (20× magnification) perfilter, aided by ImageJ.

PI3 Kinase Assay.

A PI3-Kinase Activity ELISA Kit (Echelon, K-1000s) was used. Briefly,PI3K was pulled down from whole cell lysates (prepared fromapproximately 1×10⁶ cells per sample) using an PI3K antibody (anti-PI3Kp85), and the immunoprecipitates were mixed with 30 μl of KBZ reactionbuffer, which was then mixed with 30 μl of 10 μM PI(4,5)P₂ substrate,followed by incubation for 2 h at 37° C. The kinase reaction wasterminated by adding 90 μl of kinase stop solution to each reactionsolution, and 60 μl of each stopped kinase reaction solution wastransferred together with 60 μl of PIP₃ detector to each well in theincubation plate. After incubation at room temperature for 60 min, 100μl per sample from the incubation plate was transferred to thecorresponding wells of the detection plate and incubated for 60 min atroom temperature. The plates were washed with TBST and then incubatedwith the HRP-conjugated secondary detector for 30 min, followed bywashing with TBST, and the immobilized HRP was measured by a standardcolorimetric assay, using 3,3′,5,5′-tetramethylbenzedine as a substrate.

Src Kinase Assay.

Src activity in cell lysates was measured using the Universal TyrosineKinase Assay Kit (TaKaRa, #MK410). Briefly, lysates (prepared fromapproximately 1×10⁶ cells per sample) were pre-cleared with proteinA-agarose beads prior to IP with a Src antibody. The immunoprecipitateswere washed and incubated with 10 mM β-mercaptoethanol in 150 μl ofkinase reaction solution. Each sample (40 μl) was mixed with 10 μl of 40mM ATP-2Na solution, which was transferred to microtiter plate wellscoated with a PTK substrate, followed by incubation at 37° C. for 30min. After wash with TBST, an HRP-conjugated anti-phosphotyrosine (PY20)solution was added to each well and incubated for 30 min at 37° C. Afteranother round of wash with TBST, the immobilized HRP was measured by astandard colorimetric assay, using 3,3′,5,5′-tetramethylbenzedine as asubstrate.

MTT Cell Proliferation Assay.

Cells were grown in 96-well plates (500 CHO-K1 cells or CHO-K1/ErbB2cells per well, 2,000 BT-474 cells per well; 150 μl medium per well)overnight and then treated with vehicle, PEPD, G278D-PEPD or trastuzumabin 200 μl medium per well for 72 h, followed by incubation with MTT (9.2mM in medium) at 37° C. for 3 h. The cells were then washed with PBS andmixed with dimethyl sulfoxide (150 μl per well), and the cell densitywas determined by measuring the reduction of MTT to formazanspectroscopically at 570 nm.

Statistical Analysis.

Student t-test and ANOVA were used for two-group comparison andmulti-group comparison, respectively. All tests were two-sided andperformed at a nominal significance level of 0.05, i.e. P value of 0.05or lower was considered statistically significant.

While the invention has been described through illustrative examples,routine modifications will be apparent to those skilled in the art,which modifications are intended to be within the scope of theinvention.

We claim:
 1. A method for therapy of ErbB2-positive cancer in anindividual, the method comprising selecting an individual for thetherapy based on a determination of ErbB-2 positive cancer cells in asample of a tumor from the individual, and subsequently inhibiting thegrowth of the tumor by administering to the individual an effectiveamount of a composition comprising peptidase D (PEPD) comprising amutation of glycine at position 278 of SEQ ID NO:1, such that growth ofthe ErbB2-positive tumor is inhibited.
 2. The method of claim 1, furthercomprising administering a coagulation inhibitor to the individual. 3.The method of claim 1, wherein the PEPD is a component of a fusionprotein.
 4. The method of claim 1 wherein the PEPD is conjugated to achemotherapeutic agent.
 5. The method of claim 1, wherein the mutationof the glycine at position 278 of SEQ ID NO:1 is a G278D mutation. 6.The method of claim 5, further comprising administering a coagulationinhibitor to the individual.